Automated Synthesis of Small Molecules Using Chiral, Non-Racemic Boronates

ABSTRACT

Provided are methods for making and using chiral, non-racemic protected organoboronic acids, including pinene-derived iminodiacetic acid (PIDA) boronates, to direct and enable stereoselective synthesis of organic molecules. Also provided are methods for purifying PIDA boronates from solution. Also provided are methods for deprotection of boronic acids from their PIDA ligands. The purification and deprotection methods may be used in conjunction with methods for coupling or otherwise reacting boronic acids. Iterative cycles of deprotection, coupling, and purification can be performed to synthesize chiral, non-racemic compounds. The methods are suitable for use in an automated chemical synthesis process. Also provided is an automated small molecule synthesizer apparatus for performing automated stereoselective synthesis of chiral, non-racemic small molecules using iterative cycles of deprotection, coupling, and purification.

RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.16/255,453, filed Jan. 23, 2019; which is a continuation of U.S. patentapplication Ser. No. 15/207,196, filed Jul. 11, 2016, now U.S. Pat. No.10,239,824, which is a continuation of U.S. patent application Ser. No.14/692,088, filed Apr. 21, 2015, now U.S. Pat. No. 9,388,131, which is adivisional of U.S. patent application Ser. No. 14/112,985, filed Dec.12, 2013, now U.S. Pat. No. 9,012,658, which is the United StatesNational Stage Application of International Patent Application No.PCT/US2012/035247, filed Apr. 26, 2012, which claims the benefit ofpriority to U.S. Provisional Patent Application Ser. No. 61/479,596,filed Apr. 27, 2011; and U.S. Provisional Patent Application Ser. No.61/590,225, filed Jan. 24, 2012.

STATEMENT OF GOVERNMENT SUPPORT

This invention was made with government support under CAREER Award No.0747778 awarded by the National Science Foundation. The government hascertain rights in the invention.

BACKGROUND OF THE INVENTION

Similar to peptides, oligonucleotides, and oligosaccharides, most smallmolecule natural products are modular in their constitution. Like theaforementioned oligomers, the majority of naturally occurring smallmolecules are biosynthesized via the sequential coupling of bifunctionalbuilding blocks. Specifically, polyketides are derived from multiplemalonyl-CoA and/or methylmalonyl-CoA units, non-ribosomal peptides arebuilt from amino acids, polyterpenes are stitched together fromisopentenyl pyrophosphate and/or dimethylallyl pyrophosphate buildingblocks, and fatty acids are prepared from fragments of malonyl-CoA.Other classes of modular natural products result from the oxidativecoupling of common building blocks, such as shikimic acid, amino acids,and/or their respective derivatives.

With peptides and oligonucleotides, and increasingly witholigosaccharides, the inherent modularity is now routinely harnessed toenable fully automated syntheses from suitably protected bifunctionalbuilding blocks (R. B. Merrifield, Science 1965, 150, 178-185; M. H.Caruthers, Science 1985, 24, 799; and O. J. Plante, M. R. Palmacci, P.H. Seeberger, Science 2001, 291, 1523). As a direct result of theseadvances, research in these areas is primarily focused on discoveringand understanding new molecular function. In stark contrast, despitetremendous advances over the course of nearly two centuries, thelaboratory synthesis of small molecules remains a relatively complex,inflexible, and non-systematized process practiced almost exclusively byhighly-trained specialists. (For pioneering developments in theautomated synthesis of small molecules via polymer-assistance and/orflow chemistry, see: a) C. H. Hornung, M. R. Mackley, I. R. Baxendale,and S. V. Ley, Org. Proc. Res. Dev. 2007, 11, 399-405; b) Nikzad Nikbin,Mark Ladlow, and Steven V. Ley, Org. Process Res. Dev. 2007, 11,458-462; and c) S. France, D. Bernstein, A. Weatherwax, and T. Lectka,Org. Lett. 2005, 7, 3009-3012.) Thus, research in this area is stillheavily weighted towards synthesis. Given the special properties of manysmall molecules that make them uniquely suited for a wide range ofapplications in science, engineering, and medicine, increased access tothese compounds via a highly general and automated synthesis platformthat is accessible to the non-expert would be highly enabling.Ultimately, such a process could help shift the primary focus from thesynthesis of small molecules to the discovery and understanding ofimportant small molecule functions.

Organoboron compounds have had a profound impact on organic synthesis.Their unique reactivity has made them among the most versatileorganometallic intermediates (boronate building blocks) for theconstruction of complex organic molecules.

The Suzuki-Miyaura reaction is a palladium- or nickel-catalyzedcross-coupling between a boronic acid or a boronic ester and anorganohalide or an organo-pseudohalide. Miyaura et al. (1995) Chem Rev95:2457-83. This cross coupling transformation is a powerful method forC—C bond formation in complex molecule synthesis. The reaction istolerant of functional groups and has become increasingly general andwidespread in its use for coupling of organic compounds. Barder et al.(2005) J Am Chem Soc 127:4685-96; Billingsley et al. (2007) J Am ChemSoc 129:3358-66; Littke et al. (2000) J Am Chem Soc 122:4020-8; Nicolaouet al. (2005) Angew Chem Int Ed 44:4442-89.

Boronic acids, on the other hand, are notoriously sensitive to manycommon reagents. Hall D G, Boronic Acids, Wiley-VCH, Germany, 2005, pp3-14; Tyrell et al. (2003) Synthesis 4:469-83. It is therefore typicalto introduce the boronic acid functional group during the last step of abuilding block synthesis. However, many of the methods for doing so(hydroboration, trapping organometallic reagents with trimethylborate,etc.) are intolerant to a variety of common functional groups, such asalcohols, aldehydes, ketones, alkynes and olefins. This makes thesynthesis of structurally complex boronic acid building blocks quitechallenging.

Conventional boronic acids are characterized by sp²-hybridized boroncovalently linked to a carbon atom of an organic moiety of interest.Incompatibility of most oxidants with these boronic acids represent asignificant limitation because it severely restricts the ability tomodify the organic moiety while retaining the carbon-boron bond.

Recently there has been keen interest in the development of protectinggroups for the boronic acid functional group. A compound that includes aprotected boronic acid and another functional group can undergo chemicaltransformations of the other functional group without chemicallytransforming the boron. Removal of the protecting group (deprotection)then provides the free boronic acid, which can undergo a Suzuki-Miyaurareaction to cross-couple the compound with an organohalide or anorgano-pseudohalide.

Toward this end, Molander and Ribagorda described potassiumorganotrifluoroborates useful in Suzuki-Miyaura cross-coupling reactionsand epoxidation reactions. Molander et al. (2003) J Am Chem Soc125:11148-9.

More recently, N-methyliminodiacetic acid (MIDA) “rigid cage” boronateshave been described as a highly versatile platform for synthesizingboronate building blocks. US 2009/0030238 (incorporated herein byreference). These MIDA boronates are characterized by the presence ofboron having sp³ hybridization covalently linked to a carbon atom of anorganic moiety of interest, wherein the boron is remarkably stable inthe face of harsh chemical conditions capable of transforming thefunctional group, yet deprotection is effectively achieved using mildaqueous basic conditions (e.g., treatment with 1 M aqueous sodiumhydroxide in tetrahydrofuran for 10 minutes). Dozens of MIDA boronatesare now commercially available from Aldrich.

Many biologically active compounds and pharmaceuticals are synthesizedas racemic mixtures, while most, if not all, of the desired biologicalactivity is typically associated with only one enantiomer of suchcompounds. It is, therefore, not surprising that there is tremendousinterest in being able to synthesize organic molecules with directedstereochemistry, including, for example, for high throughput screeningfor biologically relevant activity.

A building-block approach to small molecule synthesis is an attractivestrategy for constructing specific complex molecules as well as forgenerating libraries of compounds. In an idealized form of thebuilding-block approach to small molecule synthesis, off-the-shelfsubunits having all the required functional groups pre-installed in thecorrect oxidation states and with the desired stereochemicalrelationships are brought together using a single reaction iteratively.

SUMMARY OF THE INVENTION

One aspect of the invention pertains to stereoisomerically enriched orsubstantially pure chiral protected organoboronic acids and theirsynthesis, characteristics, and use in directing and enablingstereoselective synthesis of organic molecules, including, in certainembodiments, their use in directing and enabling stereoselectivesynthesis of organic molecules in an automated manner. Astereoisomerically enriched or substantially pure chiral protectedorganoboronic acid includes a boron atom having sp³ hybridization, aconformationally rigid protecting group bonded to the boron atom, achiral group bonded to or forming part of the protecting group, and anorganic group bonded to the boron atom through a covalent boron-carbon(B—C) bond. The protecting group may be a trivalent group. The chiralgroup, bonded to or forming part of the protecting group, is arranged tobe in such proximity to the organic group that it can influence thestereoselectivity of a chemical transformation of the organic groupwhile it remains bonded to the boron through the boron-carbon bond.Typically, the organic group can undergo a chemical transformationwithout chemically transforming the boron atom. In one embodiment theorganic group is or includes a prochiral group.

In one embodiment the protecting group is derived from an iminodiaceticacid (IDA) in which the chiral group is a chiral moiety appended to thenitrogen of the IDA group through a covalent bond.

In one embodiment the protecting group is derived from an IDA in whichthe chiral group is part of the IDA.

In one embodiment the protecting group is derived from an IDA in whichthe IDA itself comprises a chiral group, and a second chiral moiety iscovalently bonded to the nitrogen of the IDA group.

In contrast to the stereoisomerically enriched or substantially purechiral protected organoboronic acids of the invention, conventionalprotected organoboronic acids include either a boron having sp²hybridization, a boron present in an anionic compound, or a boron bondedto a protecting group that is not conformationally rigid, for example,the potassium organotrifluoroborates described by Molander andRibagorda. Molander et al. (2003) J Am Chem Soc 125:11148-9.

Certain aspects of the invention relate to a process that iterativelyutilizes a carbon-carbon bond-forming reaction to assemble a wide rangeof small molecules from pre-fabricated building blocks. In oneembodiment, the process is an automated process. In certain embodiments,analogous to the automated preparation of peptides from suitablyprotected amino acids, the automated process involves the controlled,iterative assembly of bifunctional haloboronic acid building blocksprotected as the corresponding chiral, non-racemic N-pinene-derivediminodiacetic acid (PIDA) boronates. In certain embodiments, obviatingthe need for any covalent attachment to a solid support, purification ofintermediates is achieved by harnessing two remarkably general physicalproperties of PIDA boronates: the capacity for catch-and-releasechromatography with silica gel; and their insolubility in hexanes.

In one embodiment, the process is carried out using an apparatusspecifically suited to perform the steps of the process in an automatedfashion.

An aspect of the invention is a method of purifying a chiral,non-racemic pinene-derived iminodiacetic acid (PIDA) boronate from asolution. The method includes the steps of diluting the solution withhexane, thereby selectively precipitating the chiral, non-racemic PIDAboronate; and isolating the precipitated chiral, non-racemic PIDAboronate.

An aspect of the invention is a method of purifying a chiral,non-racemic pinene-derived iminodiacetic acid (PIDA) boronate from asolution. The method includes the steps of passing the solution througha silica plug; passing a first liquid through the silica plug; andpassing a second liquid through the silica plug, thereby eluting thechiral, non-racemic PIDA boronate in the second liquid; wherein thefirst liquid contains diethyl ether or the polarity of the first liquidis less than or equal to about the polarity of a mixture of 98.5:1.5(v/v) Et₂O:MeOH; and the polarity of the second liquid is greater thanor equal to about the polarity of tetrahydrofuran (THF).

An aspect of the invention is a method of purifying a chiral,non-racemic pinene-derived iminodiacetic acid (PIDA) boronate from asolution. The method includes the steps of diluting the solution withhexane, thereby selectively precipitating the chiral, non-racemic PIDAboronate; passing the diluted solution through a silica plug, therebydepositing the precipitated chiral, non-racemic PIDA boronate on thesilica plug; passing a first liquid through the silica plug; and passinga second liquid through the silica plug, thereby eluting the chiral,non-racemic PIDA boronate in the second liquid; wherein the first liquidcontains diethyl ether or the polarity of the first liquid is less thanor equal to about the polarity of a mixture of 98.5:1.5 (v/v) Et₂O:MeOH;and the polarity of the second liquid is greater than or equal to aboutthe polarity of tetrahydrofuran (THF).

An aspect of the invention is a method of deprotecting a chiral,non-racemic pinene-derived iminodiacetic acid (PIDA) boronate. Themethod includes the step of contacting a solution, comprising thechiral, non-racemic PIDA boronate and a solvent, with a solid-supportedammonium hydroxide reagent, thereby deprotecting the chiral, non-racemicPIDA boronate and forming a boronic acid and a PIDA.

An aspect of the invention is a method of deprotecting a chiral,non-racemic pinene-derived iminodiacetic acid (PIDA) boronate. Themethod includes the step of contacting a solution comprising the chiral,non-racemic PIDA boronate and a solvent with an aqueous solution ofNaOH, thereby deprotecting the chiral, non-racemic PIDA boronate andforming a boronic acid and a PIDA ligand.

In certain embodiments, the chiral, non-racemic PIDA boronate isrepresented by

-   -   wherein:    -   B is a boron atom having spa hybridization;    -   R* is a chiral group

of at least 90% enantiomeric excess;

-   -   R²¹ and R²² are independently selected from the group consisting        of hydrogen, alkyl, cycloalkyl, heterocyclyl, aryl, heteroaryl,        aralkyl, and heteroaralkyl; or R²¹ and R²², taken together, form        a 5-10-membered cycloalkyl or aromatic ring, or form a        5-10-membered heterocyclic or heteroaromatic ring comprising 1-3        heteroatoms independently selected from the group consisting of        N, O, and S;    -   R²³ is selected from the group consisting of hydrogen, alkyl,        cycloalkyl, heterocyclyl, aryl, heteroaryl, aralkyl, and        heteroaralkyl;    -   R¹⁰ is selected from the group consisting of

-   -   R¹¹ and each instance of R¹² are independently selected from the        group consisting of hydrogen, halogen, hydroxyl, (C1-C10)alkyl,        cycloalkyl, aryl, aralkyl, heteroaralkyl, alkoxyl, acyl,        acyloxy, aryloxy, amino, and trialkylsilyloxy; or R¹¹ and any        one instance of R¹², or any two instances of R¹², taken        together, form a 3-10-membered ring;    -   X is halogen;    -   each instance of Z is independently selected from the group        consisting of CH and N, provided that no more than two instances        of Z are N;    -   X′ is selected from the group consisting of CR⁵R⁶, O, S, and        NR⁷;    -   R¹ and R² are both hydrogen or identically selected        (C1-C3)alkyl;    -   R³ and R⁴ are both hydrogen or identically selected        (C1-C3)alkyl;    -   R⁵ and R⁶ are independently selected from the group consisting        of hydrogen, halogen, hydroxyl, (C1-C10)alkyl, cycloalkyl, aryl,        aralkyl, heteroaralkyl, alkoxyl, acyl, acyloxy, aryloxy, amino,        and trialkylsilyloxy;    -   R⁷ is selected from the group consisting of hydrogen and        (C1-C3)alkyl;    -   m is 0, 1, or 2;    -   n is 0, 1, or 2; and    -   p is 0, 1, or 2.

Additional aspects, embodiments, and advantages of the invention arediscussed below in detail.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 represents, generically, the chemical structure and reactions ofcompounds of formula (I) of the invention.

FIG. 2 represents chemical structure and reactions of stable α-borylaldehyde 4. Ipc=isopinocamphenyl. d.r.=diastereomeric ratio.

FIG. 3 is a series of variable-temperature NMR spectra of 2a and 3a.Spectra were collected in 1,1,2,2-tetrachloroethane at the indicatedtemperatures.

FIG. 4 is a drawing of one embodiment of a fully automated smallmolecule synthesizer comprising modules for (i) deprotection, (ii)cross-coupling, and (iii) purification, all of which are under thecontrol of a computer equipped with custom-designed software.

FIG. 5A depicts a design schematic of one embodiment of an automatedsmall molecule synthesizer, wherein (1) denotes solvent reservoirs; (2)denotes a drying and degassing table; (3) denotes a heating block andstir-plate; (4) denotes solenoid valves and gas manifolds; (5) denotes adeprotection table; (6) denotes a purification table; (7) denotes avalve module (with one example of a valve map shown in FIG. 5); (8)denotes main syringe pumps; (9) denotes a syringe pump for purification;and (10) denotes a syringe pump for aqueous reactions.

FIG. 5B depicts an example of the connectivity of the various pumps,valves, ports and tubes.

FIG. 6A is a drawing depicting exemplary reaction tubes and fittings.

FIG. 6B is a drawing depicting exemplary tubing and fittings.

FIG. 7 depicts an example of a valve map.

FIG. 8A is a drawing depicting an example of a three reaction tubes.

FIG. 8B depicts a schematic of a reaction tube.

FIG. 8C is a drawing depicting an example of a reaction tube.

FIG. 9 is a schematic of an example of an aqueous deprotection module.

FIG. 10A is a schematic of a precipitation chamber and silica column.

FIG. 10B is a drawing depicting an example of a precipitation chamberand silica column.

FIG. 11 depicts an example of a drying and degassing tube.

FIG. 12A depicts automated aqueous deprotection of phenyl MIDA boronateand subsequent automated cross-coupling of phenyl boronic acid with avinyl iodide bifunctional building block.

FIG. 12B depicts automated aqueous deprotection of trienyl MIDA boronateand subsequent automated cross-coupling of trienyl boronic acid with avinyl iodide bifunctional building block.

FIG. 12C depicts automated aqueous deprotection of butenyl MIDA boronateand subsequent automated cross-coupling of butenyl boronic acid with anisomeric mixture of dienyl vinyl iodide bifunctional building blocks.

FIG. 13 depicts fully automated synthesis of all-trans-retinal using anaqueous deprotection module.

FIG. 14A and FIG. 14B depict a pair of ¹H NMR spectra corresponding to(i) a mock reaction mixture comprising a PIDA boronate, and (ii) thePIDA boronate after purification from the mixture.

DETAILED DESCRIPTION OF THE INVENTION

The invention is based at least in part on the discovery of apinene-derived iminodiacetic acid (PIDA) ligand that enables the facilesynthesis of a wide range of versatile Csp³ chiral boronate buildingblocks in a highly stereocontrolled fashion. Together, theconformational rigidity of the iminodiacetic acid framework protectingthe boron atom having sp³ hybridization and the chirality of the groupappended to the nitrogen atom, result in effective transfer ofstereochemical information during functionalizations of the boronate dueto enforced proximity. See FIG. 1.

Beginning with their discovery of the PIDA ligand, the inventors havedeveloped and characterized a class of chiral IDA-based ligands andcorresponding stereoisomerically enriched or substantially pure chiralorganoboronic acids useful in the preparation and use of boronatebuilding blocks for organic synthesis.

Certain aspects of the present invention are directed to methods andapparatuses suitable for the automated stereoselective synthesis ofsmall molecules comprising at least one chiral center. In certainembodiments, the small molecules are prepared by using a single reactioniteratively to unite a collection of bifunctional building blocks havingall of the required functionality, oxidation states, and stereochemistrypre-installed.

Definitions

The following definitions are included to provide a clear and consistentunderstanding of the specification and claims.

The articles “a” and “an” are used herein to refer to one or to morethan one (i.e., to at least one) of the grammatical object of thearticle. By way of example, “an element” means one element or more thanone element.

The phrase “and/or,” as used herein in the specification and in theclaims, should be understood to mean “either or both” of the elements soconjoined, i.e., elements that are conjunctively present in some casesand disjunctively present in other cases. Multiple elements listed with“and/or” should be construed in the same fashion, i.e., “one or more” ofthe elements so conjoined. Other elements may optionally be presentother than the elements specifically identified by the “and/or” clause,whether related or unrelated to those elements specifically identified.Thus, as a non-limiting example, a reference to “A and/or B”, when usedin conjunction with open-ended language such as “comprising” can refer,in one embodiment, to A only (optionally including elements other thanB); in another embodiment, to B only (optionally including elementsother than A); in yet another embodiment, to both A and B (optionallyincluding other elements); etc.

As used herein in the specification and in the claims, “or” should beunderstood to have the same meaning as “and/or” as defined above. Forexample, when separating items in a list, “or” or “and/or” shall beinterpreted as being inclusive, i.e., the inclusion of at least one, butalso including more than one, of a number or list of elements, and,optionally, additional unlisted items. Only terms clearly indicated tothe contrary, such as “only one of” or “exactly one of,” or, when usedin the claims, “consisting of,” will refer to the inclusion of exactlyone element of a number or list of elements. In general, the term “or”as used herein shall only be interpreted as indicating exclusivealternatives (i.e., “one or the other but not both”) when preceded byterms of exclusivity, such as “either,” “one of,” “only one of,” or“exactly one of” “Consisting essentially of,” when used in the claims,shall have its ordinary meaning as used in the field of patent law.

As used herein in the specification and in the claims, the phrase “atleast one,” in reference to a list of one or more elements, should beunderstood to mean at least one element selected from any one or more ofthe elements in the list of elements, but not necessarily including atleast one of each and every element specifically listed within the listof elements and not excluding any combinations of elements in the listof elements. This definition also allows that elements may optionally bepresent other than the elements specifically identified within the listof elements to which the phrase “at least one” refers, whether relatedor unrelated to those elements specifically identified. Thus, as anon-limiting example, “at least one of A and B” (or, equivalently, “atleast one of A or B,” or, equivalently “at least one of A and/or B”) canrefer, in one embodiment, to at least one, optionally including morethan one, A, with no B present (and optionally including elements otherthan B); in another embodiment, to at least one, optionally includingmore than one, B, with no A present (and optionally including elementsother than A); in yet another embodiment, to at least one, optionallyincluding more than one, A, and at least one, optionally including morethan one, B (and optionally including other elements); etc.

It should also be understood that, unless clearly indicated to thecontrary, in any methods claimed herein that include more than one stepor act, the order of the steps or acts of the method is not necessarilylimited to the order in which the steps or acts of the method arerecited.

In the claims, as well as in the specification above, all transitionalphrases such as “comprising,” “including,” “carrying,” “having,”“containing,” “involving,” “holding,” “composed of,” and the like are tobe understood to be open-ended, i.e., to mean including but not limitedto. Only the transitional phrases “consisting of” and “consistingessentially of” shall be closed or semi-closed transitional phrases,respectively, as set forth in the United States Patent Office Manual ofPatent Examining Procedures, Section 2111.03.

For the purposes of this invention, the chemical elements are identifiedin accordance with the Periodic Table of the Elements, CAS version,Handbook of Chemistry and Physics, 67th Ed., 1986-1987, inside cover.

The term “acyl” or “acyl group” means any group or radical of the form—C(═O)R, where R is an organic group. An example of the acyl group isthe acetyl group (—C(═O)CH₃).

The term “acyloxy” or “acyloxy group” as used herein refers to means anacyl group, as defined herein, appended to the parent molecular moietythrough an oxygen atom.

The term “alkenyl” or “alkenyl group” means a group formed by removing ahydrogen from a carbon of an alkene, where an alkene is an acyclic orcyclic compound consisting entirely of hydrogen atoms and carbon atoms,and including at least one carbon-carbon double bond. An alkenyl groupmay include one or more substituent groups.

The term “alkoxy” or “alkoxy group” as used herein means an alkyl group,as defined herein, appended to the parent molecular moiety through anoxygen atom. Representative examples of alkoxy include, but are notlimited to, methoxy, ethoxy, propoxy, 2-propoxy, butoxy, tert-butoxy,pentyloxy, and hexyloxy. The terms “alkyenyloxy”, “alkynyloxy”,“carbocyclyloxy”, and “heterocyclyloxy” are likewise defined.

The term “alkyl” or “alkyl group” means a group formed by removing ahydrogen from a carbon of an alkane, where an alkane is an acyclic orcyclic compound consisting entirely of hydrogen atoms and saturatedcarbon atoms. In various embodiments an alkyl contains 1 to 20, 1 to 15,or 1 to 10 carbon atoms. In one embodiment an alkyl contains 1 to 3carbon atoms. Representative examples of alkyl include, but are notlimited to, methyl, ethyl, n-propyl, iso-propyl, n-butyl, sec-butyl,iso-butyl, tert-butyl, n-pentyl, isopentyl, neopentyl, n-hexyl,2-methylcyclopentyl, 1-(1-ethylcyclopropyl)ethyl and 1-cyclohexylethyl.An alkyl group may include one or more substituent groups.

The term “alkynyl group” means a group formed by removing a hydrogenfrom a carbon of an alkyne, where an alkyne is an acyclic or cycliccompound consisting entirely of hydrogen atoms and carbon atoms, andincluding at least one carbon-carbon triple bond. An alkynyl group mayinclude one or more substituent groups.

The term “amino”, “amino group”, or “amine” as used herein refers to—NH₂ and substituted derivatives thereof wherein one or both of thehydrogens are independently replaced with substituents selected from thegroup consisting of alkyl, haloalkyl, fluoroalkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, aralkyl, heteroaryl, heteroaralkyl,alkylcarbonyl, haloalkylcarbonyl, fluoroalkylcarbonyl, alkenylcarbonyl,alkynylcarbonyl, carbocyclylcarbonyl, heterocyclylcarbonyl,arylcarbonyl, aralkylcarbonyl, heteroarylcarbonyl,heteroaralkylcarbonyl, sufonyl, and sulfinyl groups; or when bothhydrogens together are replaced with an alkylene group (to form a ringwhich contains the nitrogen). Representative examples include, but arenot limited to methylamino, acetylamino, and dimethylamino.

The term “amido” as used herein means an amino group, as defined herein,appended to the parent molecular moiety through a carbonyl.

The term “arylalkyl” or “aralkyl” as used herein means an aryl group, asdefined herein, appended to the parent molecular moiety through an alkylgroup, as defined herein. Representative examples of aralkyl include,but are not limited to, benzyl, 2-phenylethyl, 3-phenylpropyl, and2-naphth-2-ylethyl.

The term “aromatic” or “aromatic group” refers to a planar or polycyclicstructure characterized by a cyclically conjugated molecular moietycontaining 4n+2 electrons, wherein n is the absolute value of aninteger. Aromatic molecules containing fused, or joined, rings also arereferred to as bicyclic aromatic rings. For example, bicyclic aromaticrings containing heteroatoms in a hydrocarbon ring structure arereferred to as bicyclic heteroaryl rings.

The term “aryl” or “aryl group” means a group formed by removing ahydrogen from a ring carbon atom of an aromatic hydrocarbon. An arylgroup may by monocyclic or polycyclic and may include one or moresubstituent groups.

The term “aryloxy” or “aryloxy group” as used herein means an arylgroup, as defined herein, appended to the parent molecular moietythrough an oxygen atom. The term “heteroaryloxy” or “heteroaryloxygroup” as used herein means a heteroaryl group, as defined herein,appended to the parent molecular moiety through an oxygen atom. Anaryloxy group may include one or more substituent groups.

The term “azido” as used herein means a —N₃ group.

The term “carbonyl” as used herein refers to a —C(═O)— group.

The term “chemical transform” of a substance means a product of achemical transformation of the substance, where the product has achemical structure different from that of the substance.

The term “chemical transformation” means the conversion of a substanceinto a product, irrespective of reagents or mechanisms involved.

The term “cyano” as used herein means a —C≡N group.

The term “cyclic” pertains to compounds and/or groups which have one ormore rings (e.g., spiro, fused, bridged).

The term “cycloalkyl” or “cycloalkyl group” is a subset of alkyl whichrefers to a cyclic hydrocarbon radical containing from 3 to 15, 3 to 10,or 3 to 7 carbon atoms. Representative examples of cycloalkyl include,but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, andcyclohexyl. A cycloalkyl group may include one or more substituentgroups.

The term “enantiomeric excess” (ee) means the absolute differencebetween the mole fraction of each enantiomer.

The term “functional group” means an atom or collection of atoms in amolecule that are responsible for characteristic chemical reactions ofthe molecule. Nonlimiting examples of functional groups include halogen,alcohol (—OH), aldehyde (—CH═O), ketone (—C(═O)—), carboxylic acid(—C(═O)OH), thiol (—SH), sulfone, sulfoxide, amine, phosphine,phosphite, phosphate, and combinations thereof. Of particular interestas functional groups in connection with the invention are alkenyl(olefinic) groups. Additional examples of organic groups includingfunctional groups that may be present in a protected organoboronic acidare illustrated or described throughout the present application.

The term “group” means a linked collection of atoms or a single atomwithin a molecular entity, where a molecular entity is anyconstitutionally or isotopically distinct atom, molecule, ion, ion pair,radical, radical ion, complex, conformer, etc., identifiable as aseparately distinguishable entity. The description of a group as being“formed by” a particular chemical transformation does not imply thatthis chemical transformation is involved in making the molecular entitythat includes the group.

The term “halogen” means —F, —Cl, —Br or —I.

The term “heteroalkenyl” or “heteroalkenyl group” means a group formedby removing a hydrogen from a carbon of a heteroalkene, where aheteroalkene is an acyclic or cyclic compound consisting entirely ofhydrogen atoms, carbon atoms, and one or more heteroatoms, and includingat least one carbon-carbon double bond. A heteroalkenyl group mayinclude one or more substituent groups.

The term “heteroalkyl group” means a group formed by removing a hydrogenfrom a carbon of a heteroalkane, where a heteroalkane is an acyclic orcyclic compound consisting entirely of hydrogen atoms, saturated carbonatoms, and one or more heteroatoms. A heteroalkyl group may include oneor more substituent groups.

The term “heteroalkynyl” or “heteralkynyl group” means a group formed byremoving a hydrogen from a carbon of a heteroalkyne, where aheteroalkyne is an acyclic or cyclic compound consisting entirely ofhydrogen atoms, carbon atoms and one or more heteroatoms, and includingat least one carbon-carbon triple bond. A heteroalkynyl group mayinclude one or more substituent groups.

The term “heteroaralkyl”, “heteroaralkyl group”, “heteroarylalkyl”, or“heteroarylalkyl group” as used herein means a heteroaryl, as definedherein, appended to the parent molecular moiety through an alkyl group,as defined herein. Representative examples of heteroarylalkyl include,but are not limited to, pyridin-3-ylmethyl and 2-(thien-2-yl)ethyl. Aheteroaralkyl group may include one or more substituent groups.

The term “heteroaromatic” or “heteroaromatic group” as used herein meansan aromatic group as defined herein, in which at least one carbon atomis replaced by a heteroatom. Representative examples of heteroaromaticgroups include, without limitation, pyrrolyl, furanyl, thiophenyl,imidazolyl, oxazolyl, thiazolyl, pyrazolyl, pyridinyl, pyrimidinyl,purinyl, quinolinyl, isoquinolinyl, and carbazolyl. A heteroaromaticgroup may include one or more substituent groups.

The term “heteroaryl” or “heteroaryl group” as used herein means aradical of aromatic ring systems, including, but not limited to,monocyclic, bicyclic and tricyclic rings, which have 3 to 12 atomsincluding at least one heteroatom, such as nitrogen, oxygen, or sulfur.Representative examples of heteroaryl groups include, withoutlimitation, aminobenzimidazolyl, benzimidazolyl, azaindolyl,benzo(b)thienyl, benzimidazolyl, benzofuranyl, benzoxazolyl,benzothiazolyl, benzothiadiazolyl, benzotriazolyl, benzoxadiazolyl,furanyl, imidazolyl, imidazopyridinyl, indolyl, indolinyl, indazolyl,isoindolinyl, isoxazolyl, isothiazolyl, isoquinolinyl, oxadiazolyl,oxazolyl, purinyl, pyranyl, pyrazinyl, pyrazolyl, pyridinyl,pyrimidinyl, pyrrolyl, pyrrolo[2,3-d]pyrimidinyl,pyrazolo[3,4-d]pyrimidinyl, quinolinyl, quinazolinyl, triazolyl,thiazolyl, thiophenyl, tetrahydroindolyl, tetrazolyl, thiadiazolyl,thienyl, thiomorpholinyl, triazolyl or tropanyl. The heteroaryl groupsof the invention may include one or more substituent groups.

The term “heteroatom” means any atom that is not carbon or hydrogen. Incertain embodiments a heteroatom is an atom selected from any ofnitrogen, oxygen, sulfur, and phosphorus.

The term “heterocyclyl”, “heterocyclic”, or “heterocyclic group” as usedherein refers to a radical of a non-aromatic ring system, including, butnot limited to, monocyclic, bicyclic and tricyclic rings, which can becompletely saturated or which can contain one or more units ofunsaturation, and has 3 to 12 atoms including at least one heteroatom,such as nitrogen, oxygen, or sulfur. For the avoidance of doubt, thedegree of unsaturation does not result in an aromatic ring system. Forpurposes of exemplification, which should not be construed as limitingthe scope of this invention, the following are examples of heterocyclicrings: aziridinyl, azirinyl, oxiranyl, thiiranyl, thiirenyl, dioxiranyl,diazirinyl, azetyl, oxetanyl, oxetyl, thietanyl, thietyl, diazetidinyl,dioxetanyl, dioxetenyl, dithietanyl, dithietyl, furyl, dioxalanyl,pyrrolyl, oxazolyl, thiazolyl, imidazolyl, oxadiazolyl, thiadiazolyl,triazolyl, triazinyl, isothiazolyl, isoxazolyl, thiophenyl, pyrazolyl,tetrazolyl, pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, triazinyl,tetrazinyl, quinolinyl, isoquinolinyl, quinoxalinyl, quinazolinyl,pyridopyrazinyl, benzoxazolyl, benzothiophenyl, benzimidazolyl,benzothiazolyl, benzoxadiazolyl, benzthiadiazolyl, indolyl,benztriazolyl, naphthyridinyl, azepines, azetidinyl, morpholinyl,oxopiperidinyl, oxopyrrolidinyl, piperazinyl, piperidinyl, pyrrolidinyl,quinicludinyl, thiomorpholinyl, tetrahydropyranyl and tetrahydrofuranyl.The heterocyclyl groups of the invention may include one or moresubstituent groups.

The term “heteroaryl group” means a group formed by replacing one ormore methine (—C═) and/or vinylene (—CH═CH—) groups in an aryl groupwith a trivalent or divalent heteroatom, respectively. A heteroarylgroup may by monocyclic or polycyclic and may include one or moresubstituent groups.

The term “hydroxyl” or “hydroxyl group” as used herein means an —OHgroup.

The term “organic group” means a group containing at least one carbonatom.

The term “organoboronic acid” means a compound represented by R—B(OH)₂,where R is an organic group that is bonded to the boron through aboron-carbon bond.

The term “phosphinyl” as used herein includes —PH₃ and substitutedderivatives thereof wherein one, two or three of the hydrogens areindependently replaced with substituents selected from the groupconsisting of alkyl, haloalkyl, fluoroalkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, aralkyl, heteroaryl, heteroaralkyl,alkoxy, haloalkoxy, fluoroalkyloxy, alkenyloxy, alkynyloxy,carbocyclyloxy, heterocyclyloxy, aryloxy, aralkyloxy, heteroaryloxy,heteroaralkyloxy, and amino.

The term “phosphoryl” as used herein refers to —P(═O)OH₂ and substitutedderivatives thereof wherein one or both of the hydroxyls areindependently replaced with substituents selected from the groupconsisting of alkyl, haloalkyl, fluoroalkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, aralkyl, heteroaryl, heteroaralkyl,alkoxy, haloalkoxy, fluoroalkyloxy, alkenyloxy, alkynyloxy,carbocyclyloxy, heterocyclyloxy, aryloxy, aralkyloxy, heteroaryloxy,heteroaralkyloxy, and amino.

The term “protected organoboronic acid” means a chemical transform of anorganoboronic acid, in which the boron has a lower chemical reactivityrelative to the original organoboronic acid.

The term “silyl” as used herein includes H₃Si— and substitutedderivatives thereof wherein one, two or three of the hydrogens areindependently replaced with substituents selected from alkyl, haloalkyl,fluoroalkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, aralkyl,heteroaryl, and heteroaralkyl. Representitive examples includetrimethylsilyl (TMS), tert-butyldiphenylsilyl (TBDPS),tert-butyldimethylsilyl (TBS/TBDMS), triisopropylsilyl (TIPS), and[2-(trimethylsilyl)ethoxy]methyl (SEM).

The term “sp³ hybridization” means that an atom is bonded and/orcoordinated in a configuration having a tetrahedral character of atleast 50%. For tetracoordinate boron atoms, the tetrahedral character ofthe boron atom is calculated by the method of Höpfl, H. (1999) JOrganomet Chem 581:129-49. In this method, the tetrahedral character(THC) is defined as:

THC_(DA)(%)=100×(1−(Σ_(n=1-6)|109.5−θ_(n)|°/90°

where θ_(n) is one of the six bond angles of the boron atom.

The term “substituent” or “substituent group” means a group thatreplaces one or more hydrogen atoms in a molecular entity. Except as maybe specified otherwise, substituent groups can include, withoutlimitation, alkyl, alkenyl, alkynyl, halo, haloalkyl, fluoroalkyl,hydroxy, alkoxy, alkyenyloxy, alkynyloxy, carbocyclyloxy,heterocyclyloxy, haloalkoxy, fluoroalkyloxy, sulfhydryl, alkylthio,haloalkylthio, fluoroalkylthio, alkyenylthio, alkynylthio, sulfonicacid, alkylsulfonyl, haloalkylsulfonyl, fluoroalkylsulfonyl,alkenylsulfonyl, alkynylsulfonyl, alkoxysulfonyl, haloalkoxysulfonyl,fluoroalkoxysulfonyl, alkenyloxysulfonyl, alkynyloxysulfony,aminosulfonyl, sulfinic acid, alkylsulfinyl, haloalkylsulfinyl,fluoroalkylsulfinyl, alkenylsulfinyl, alkynylsulfinyl, alkoxysulfinyl,haloalkoxysulfinyl, fluoroalkoxysulfinyl, alkenyloxysulfinyl,alkynyloxysulfiny, aminosulfinyl, formyl, alkylcarbonyl,haloalkylcarbonyl, fluoroalkylcarbonyl, alkenylcarbonyl,alkynylcarbonyl, carboxyl, alkoxycarbonyl, haloalkoxycarbonyl,fluoroalkoxycarbonyl, alkenyloxycarbonyl, alkynyloxycarbonyl,alkylcarbonyloxy, haloalkylcarbonyloxy, fluoroalkylcarbonyloxy,alkenylcarbonyloxy, alkynylcarbonyloxy, alkylsulfonyloxy,haloalkylsulfonyloxy, fluoroalkylsulfonyloxy, alkenylsulfonyloxy,alkynylsulfonyloxy, haloalkoxysulfonyloxy, fluoroalkoxysulfonyloxy,alkenyloxysulfonyloxy, alkynyloxysulfonyloxy, alkylsulfinyloxy,haloalkylsulfinyloxy, fluoroalkylsulfinyloxy, alkenylsulfinyloxy,alkynylsulfinyloxy, alkoxysulfinyloxy, haloalkoxysulfinyloxy,fluoroalkoxysulfinyloxy, alkenyloxysulfinyloxy, alkynyloxysulfinyloxy,aminosulfinyloxy, amino, amido, aminosulfonyl, aminosulfinyl, cyano,nitro, azido, phosphinyl, phosphoryl, silyl, and silyloxy.

The term “sulfinyl” as used herein refers to a —S(═O)— group.

The term “sulfonyl” as used herein refers to a —S(═O)₂— group.

The term “trialkylsilyloxy” or “trialkylsilyloxy group” as used hereinrefers to a trialkylysilyl group, as defined herein, appended to theparent molecular moiety through an oxygen atom.

Exemplary Chiral IDA Compounds

An aspect of the invention is novel iminodiacetic acid (IDA) molecules.The novel IDA molecules of the invention include at least one chiralcarbon atom or have appended to them through the nitrogen atom asubstituent characterized by having at least one chiral carbon atom. Inone embodiment the novel IDA molecules of the invention include at leastone chiral carbon atom and have appended to them through the nitrogenatom a substituent characterized by having at least one chiral carbonatom.

In one embodiment the IDA molecules of the invention have appended tothem through the nitrogen atom a chiral group R*. In one embodiment theIDA molecules of the invention have appended to them through thenitrogen atom a chiral group R* of at least 90% enantiomeric excess.

In one embodiment an IDA molecule of the invention is a compound offormula (III)

wherein:

R* is a chiral group

R²¹ and R²² are independently selected from the group consisting ofhydrogen, alkyl, cycloalkyl, heterocyclyl, aryl, heteroaryl, aralkyl,and heteroaralkyl; or R²¹ and R²², taken together, form a 5-10-memberedcycloalkyl or aromatic ring, or form a 5-10-membered heterocyclic orheteroaromatic ring comprising 1-3 heteroatoms independently selectedfrom the group consisting of N, O, and S;

R²³ is selected from the group consisting of hydrogen, alkyl,cycloalkyl, heterocyclyl, aryl, heteroaryl, aralkyl, and heteroaralkyl;

R¹ and R² are both hydrogen or identically selected (C1-C3)alkyl;

R³ and R⁴ are both hydrogen or identically selected (C1-C3)alkyl; and

m is an integer 0, 1, or 2.

In one embodiment the IDA molecule in accordance with formula (III) isnot

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R²¹ and R²², taken together, form a 5-10-memberedcycloalkyl or aromatic ring, or form a 5-10-membered heterocyclic orheteroaromatic ring comprising 1-3 heteroatoms independently selectedfrom the group consisting of N, O, and S.

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, m in any one of the foregoing embodiments is 0.

In one embodiment, R* in any one of the foregoing embodiments is achiral group of at least 90% enantiomeric excess. In one embodiment, R*in any one of the foregoing embodiments is a chiral group of at least95% enantiomeric excess. In one embodiment, R* in any one of theforegoing embodiments is a chiral group of at least 98% enantiomericexcess. In one embodiment, R* in any one of the foregoing embodiments isa chiral group of at least 99% enantiomeric excess.

In an alternative embodiment, all else being the same, R¹ and R², and/orR³ and R⁴, are independently selected from the group consisting ofhydrogen and (C1-C3)alkyl.

In one embodiment, an IDA molecule of the invention is selected from thegroup consisting of

In one embodiment, an IDA molecule of the invention is selected from thegroup consisting of

In one embodiment, an IDA molecule of the invention is selected from thegroup consisting of

In one embodiment the IDA molecules of the invention include at leastone chiral carbon atom. In one embodiment the IDA molecules of theinvention include at least one chiral carbon atom, wherein the chiralcarbon atom is a chiral carbon atom of at least 90% enantiomeric excess.

In one embodiment an IDA molecule of the invention is a compound offormula (IV)

wherein:

R¹ and R² are both hydrogen or identically selected (C1-C3)alkyl;

R³⁰ is selected from the group consisting of hydrogen and (C1-C3)alkyl;and

q is 1 or 2.

In one embodiment, the IDA molecule in accordance with formula (IV) isnot

In one embodiment, q is 1 in any one of the foregoing embodiments.

In one embodiment the carbon atom marked “*” in formula (IV) is a chiralcarbon atom of at least 90% enantiomeric excess. In one embodiment, thecarbon atom marked “*” in formula (IV) in any one of the foregoingembodiments is a chiral carbon of at least 95% enantiomeric excess. Inone embodiment, the carbon atom marked “*” in formula (IV) in any one ofthe foregoing embodiments is a carbon atom of at least 98% enantiomericexcess. In one embodiment, the carbon atom marked “*” in formula (IV) inany one of the foregoing embodiments is a carbon atom of at least 99%enantiomeric excess.

In an alternative embodiment, all else being the same, R¹ and R² areindependently selected from the group consisting of hydrogen and(C1-C3)alkyl.

As is described in greater detail below, the foregoing IDA molecules andcertain IDA molecules similar to the foregoing may be referred to asligands and are useful for forming or preparing stereoisomericallyenriched or substantially pure chiral organoboronic acid molecules ofthe invention.

An aspect of the invention concerns certain novel stereoselectiveprotected organoboronic acid compounds. These stereoselective protectedorganoboronic acid compounds of the present invention share certainfeatures and advantages of MIDA boronate compounds disclosed in US2009/0030238, but they include the additional feature of having a chiralcarbon, present in substantial enantiomeric excess, that is part of orappended to an IDA-derived ligand in such a manner as to be able totransfer stereochemical information to the organic group due to enforcedproximity between the chiral center and the organic group.

In particular, an aspect of the invention is a compound of formula (I):

-   -   wherein:    -   B is a boron atom having spa hybridization;    -   R* is a chiral group

of at least 90% enantiomeric excess;

-   -   R²¹ and R²² are independently selected from the group consisting        of hydrogen, alkyl, cycloalkyl, heterocyclyl, aryl, heteroaryl,        aralkyl, and heteroaralkyl; or R²¹ and R²², taken together, form        a 5-10-membered cycloalkyl or aromatic ring, or form a        5-10-membered heterocyclic or heteroaromatic ring comprising 1-3        heteroatoms independently selected from the group consisting of        N, O, and S;    -   R²³ is selected from the group consisting of hydrogen, alkyl,        cycloalkyl, heterocyclyl, aryl, heteroaryl, aralkyl, and        heteroaralkyl;    -   R¹⁰ is selected from the group consisting of

-   -   R¹¹ and each instance of R¹² are independently selected from the        group consisting of hydrogen, halogen, hydroxyl, (C1-C10)alkyl,        cycloalkyl, aryl, aralkyl, heteroaralkyl, alkoxyl, acyl,        acyloxy, aryloxy, amino, and trialkylsilyloxy; or R¹¹ and any        one instance of R¹², or any two instances of R¹², taken        together, form a 3-10-membered ring;    -   X is halogen;    -   each instance of Z is independently selected from the group        consisting of CH and N, provided that no more than two instances        of Z are N;    -   X′ is selected from the group consisting of CR⁵R⁶, 0, S, and        NR⁷;    -   R¹ and R² are both hydrogen or identically selected        (C1-C3)alkyl;    -   R³ and R⁴ are both hydrogen or identically selected        (C1-C3)alkyl;    -   R⁵ and R⁶ are independently selected from the group consisting        of hydrogen, halogen, hydroxyl, (C1-C10)alkyl, cycloalkyl, aryl,        aralkyl, heteroaralkyl, alkoxyl, acyl, acyloxy, aryloxy, amino,        and trialkylsilyloxy;    -   R⁷ is selected from the group consisting of hydrogen and        (C1-C3)alkyl;    -   m is 0, 1, or 2;    -   n is 0, 1, or 2; and    -   p is 0, 1, or 2.

In an alternative embodiment, all else being the same, R¹ and R², and/orR³ and R⁴, are independently selected from the group consisting ofhydrogen and (C1-C3)alkyl.

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is selected from the group consisting of

In one embodiment, R* is selected from the group consisting of

In one embodiment, R* is selected from the group consisting of

In one embodiment, R²¹ and R²², taken together, form a 5-10-memberedcycloalkyl or aromatic ring, or form a 5-10-membered heterocyclic orheteroaromatic ring comprising 1-3 heteroatoms independently selectedfrom the group consisting of N, O, and S.

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In accordance with any one of the foregoing embodiments, in oneembodiment, R⁵ and R⁶ are independently selected from the groupconsisting of hydrogen and (C1-C3)alkyl.

In accordance with any one of the foregoing embodiments, in oneembodiment, m is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, m is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,m is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, n is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, n is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,n is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, p is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, p is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,p is 2.

In accordance with any one of the foregoing embodiments not otherwiseexcluded, in one embodiment, R¹⁰ is

n is 0, p is 0, each instance of R¹² is hydrogen, and R¹¹ is selectedfrom the group consisting of aryl and methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

n is 0, X′ is CH₂, and R¹¹ is methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

In accordance with any one of the foregoing embodiments, in oneembodiment, R* is a chiral group

of at least 95% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment, R* is a chiral group

of at least 98% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment, R* is a chiral group

of at least 99% enantiomeric excess.

It will be appreciated that R¹⁰ represents an organic group bonded tothe boron atom through a B—C bond. Alternatively or in addition toembodiments of R¹⁰ recited above, R¹⁰ can, in accordance with this andother aspects of the invention, represent any suitable radical derivedfrom a prochiral compound, including, for example, prochiral compoundsdisclosed in U.S. Pat. Nos. 4,713,380, 4,772,752, 5,068,432, and5,159,116 (all four of which are incorporated by reference) to H. C.Brown, and including, but not limited to, cis-alkenes, trans-alkenes,cycloalkenes, phenyl-substituted alkenes, heterocyclic olefins,2,3-dihydrofuran, 2,3-dihydrothiophene, 3,4-dihydro-2H-pyran,3,4-dihydro-2H-thiophan, prochiral ketones, acetylenic ketones, aralkylketones, heteroaralkyl ketones, 3,3-dimethyl-2-butanone, acetophenone,3-methyl-2-butanone, 2′-acetonapthone, 3-acetylpyridine,2-acetylthiophene, butyrophenone, isobutyrophenone, pivalophenone,1-indanone, 2-butanone, ethyl 2,2-dimethylcyclopentanone,2,2-dimethylcyclohexanone, spiro[4,4]nonan-1-one, methyl1-methyl-2-oxo-cyclopentane carboxylate, 1-methyl-2-norbornanone,haloarylalkylketone, acetylcyclohexane, 2,2-dimethylcyclopentanone,2-chloroacetophenone, methyl benzoylformate,trans-4-phenyl-3-buten-2-one, 2-cyclohexen-1-one,4-phenyl-3-butyn-2-one, and methylcyclohexanone.

Further in connection with stereoisomerically enriched or substantiallypure chiral organoboronic acid compounds of the invention, an aspect ofthe invention is a compound of formula (II):

wherein:

B is a boron atom having sp³ hybridization;

the carbon atom marked “*” is a chiral carbon atom of at least 90%enantiomeric excess;

R¹⁰ is selected from the group consisting of

-   -   R¹¹ and each instance of R¹² are independently selected from the        group consisting of hydrogen, halogen, hydroxyl, (C1-C10)alkyl,        cycloalkyl, aryl, aralkyl, heteroaralkyl, alkoxyl, acyl,        acyloxy, aryloxy, amino, and trialkylsilyloxy; or R^(H) and any        one instance of R¹², or any two instances of R¹², taken        together, form a 3-10-membered ring;    -   X is halogen;    -   each instance of Z is independently selected from the group        consisting of CH and N, provided that no more than two instances        of Z are N;    -   X′ is selected from the group consisting of CR⁵R⁶, 0, S, and        NR′;    -   R¹ and R² are both hydrogen or identically selected        (C1-C3)alkyl;    -   R⁵ and R⁶ are independently selected from the group consisting        of hydrogen, halogen, hydroxyl, (C1-C10)alkyl, cycloalkyl, aryl,        aralkyl, heteroaralkyl, alkoxyl, acyl, acyloxy, aryloxy, amino,        and trialkylsilyloxy;    -   R⁷ and RN are independently selected from the group consisting        of hydrogen and (C1-C3)alkyl;    -   n is 0, 1, or 2;    -   p is 0, 1, or 2; and    -   q is 1 or 2.

In an alternative embodiment, all else being the same, R¹ and R² areindependently selected from the group consisting of hydrogen and(C1-C3)alkyl.

In one embodiment, the compound of formula (II) is

In accordance with any one of the foregoing embodiments, in oneembodiment, n is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, n is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,n is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, p is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, p is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,p is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, q is 1. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, q is 2.

In accordance with any one of the foregoing embodiments not otherwiseexcluded, in one embodiment, R¹⁰ is

n is 0, p is 0, each instance of R¹² is hydrogen, and R^(H) is selectedfrom the group consisting of aryl and methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

n is 0, X′ is CH₂, and R¹¹ is methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

In accordance with any one of the foregoing embodiments, in oneembodiment the carbon atom marked “*” is a chiral carbon atom of atleast 95% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment the carbon atom marked “*” is achiral carbon atom of at least 98% enantiomeric excess. In accordancewith any one of the foregoing embodiments, in one embodiment the carbonatom marked “*” is a chiral carbon atom of at least 99% enantiomericexcess.

Exemplary Methods Relating to Chiral IDA Compounds

Protected organoboronic acids according to formula (I) may be preparedby reaction of an appropriate N-substituted imino-di-carboxylic acid,such as appropriate ligands described above (e.g., in accordance withformula (III)), with the corresponding unprotected boronic acid offormula (V), as illustrated in the following reaction scheme:

In a specific example, protected organoboronic acids according toformula (I) may be prepared by reaction of N-pinene-iminodiacetic acid(PIDA) with the corresponding unprotected boronic acid (V), asillustrated in the following reaction scheme:

In each case, the protected organoboronic acid may be deprotected bycontact with a mild aqueous base, to provide the free boronic acid (V).

Protected organoboronic acids according to formula (I) also may beprepared without using an isolated boronic acid as a reactant. Theboronic acid may be formed in situ, just prior to its conversion to aprotected organoboronic acid. Protected organoboronic acids also may beformed without ever forming the free boronic acid.

In one example, the boronic acid may be produced in situ, such as byhydrolysis of a boronate ester (i.e., R¹⁰—B—(OR′)(OR″), where R′ and R″are organic groups). The boronate ester may be formed, for example, byaddition of HB(OR′)(OR″) across the C—C multiple bond of an alkene or analkyne. Brown (1972) J Am Chem Soc 94:4370-1. The boronate ester alsomay be formed, for example, by a Miyaura borylation (Miyaura et al.(1997) Tet Lett 38:3447-50; Miyaura et al. (1995) J Org Chem60:7508-10); by reaction of an organohalide with an organolithiumreagent, followed by reaction with boronate triester (i.e., B(OR)₃); orby reaction of a boronate triester with an organometal reagent (i.e.,R—Li, R—Mg, R—Zn; Brown et al. (1983) Organometallics 2:1316-9. Inanother example, the boronic acid may be produced in situ, such as bytreatment of a tri-substituted borane (i.e., R¹⁰—BR′R″) withacetaldehyde (R′ and R″ are organic groups). The tri-substituted boranemay be formed, for example, by hydroborylation of an alkene or an alkynewith HBR′R″, to add the HBR′R″ across the C—C multiple bond.

In another example, a boronic halide (VI) may be reacted with a diacidor its corresponding salt to provide protected organoboronic acid (I),as illustrated in the following reaction scheme:

The boronic halide may be formed by hydroborylation of an alkene or analkyne with HBX₂ (Brown (1984) Organometallics 3:1392-5; Brown (1982) JOrg Chem 47:3808-10) or with BX₃. Soundararajan et al. (1990) J Org Chem55:2274-5. The boronic halide also may be formed by treatment of asilane such as R¹—SiR₃ with BBr₃. Qin (2002) J Am Chem Soc 124:12672-3;Qin (2004) Macromolecules 37:7123-31.

An aspect of the invention concerns a method of forming a compound offormula (I)

The method includes the step of reacting a compound represented byformula (III)

with a compound of formula (V)

R¹⁰—B(OH)₂  (V),

-   -   wherein:    -   B in formula (I) is boron having sp³ hybridization;    -   R* is a chiral group

of at least 90% enantiomeric excess;

-   -   R²¹ and R²² are independently selected from the group consisting        of hydrogen, alkyl, cycloalkyl, heterocyclyl, aryl, heteroaryl,        aralkyl, and heteroaralkyl; or R²¹ and R²², taken together, form        a 5-10-membered cycloalkyl or aromatic ring, or form a        5-10-membered heterocyclic or heteroaromatic ring comprising 1-3        heteroatoms independently selected from the group consisting of        N, O, and S;    -   R²³ is selected from the group consisting of hydrogen, alkyl,        cycloalkyl, heterocyclyl, aryl, heteroaryl, aralkyl, and        heteroaralkyl;    -   R¹⁰ is selected from the group consisting of

-   -   R¹¹ and each instance of R¹² are independently selected from the        group consisting of hydrogen, halogen, hydroxyl, (C1-C10)alkyl,        cycloalkyl, aryl, aralkyl, heteroaralkyl, alkoxyl, acyl,        acyloxy, aryloxy, amino, and trialkylsilyloxy; or R^(H) and any        one instance of R¹², or any two instances of R¹², taken        together, form a 3-10-membered ring;    -   X is halogen;    -   each instance of Z is independently selected from the group        consisting of CH and N, provided that no more than two instances        of Z are N;    -   X′ is selected from the group consisting of CR⁵R⁶, 0, S, and        NR⁷;    -   R¹ and R² are both hydrogen or identically selected        (C1-C3)alkyl;    -   R³ and R⁴ are both hydrogen or identically selected        (C1-C3)alkyl;    -   R⁵ and R⁶ are independently selected from the group consisting        of hydrogen, halogen, hydroxyl, (C1-C10)alkyl, cycloalkyl, aryl,        aralkyl, heteroaralkyl, alkoxyl, acyl, acyloxy, aryloxy, amino,        and trialkylsilyloxy;    -   R⁷ is selected from the group consisting of hydrogen and        (C1-C3)alkyl;    -   m is 0, 1, or 2;    -   n is 0, 1, or 2; and    -   p is 0, 1, or 2.

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is selected from the group consisting of

In one embodiment, R* is selected from the group consisting of

In one embodiment, R* is selected from the group consisting of

In one embodiment, R²¹ and R²², taken together, form a 5-10-memberedcycloalkyl or aromatic ring, or form a 5-10-membered heterocyclic orheteroaromatic ring comprising 1-3 heteroatoms independently selectedfrom the group consisting of N, O, and S.

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In accordance with any one of the foregoing embodiments, in oneembodiment, R⁵ and R⁶ are independently selected from the groupconsisting of hydrogen and (C1-C3)alkyl.

In accordance with any one of the foregoing embodiments, in oneembodiment, m is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, m is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,m is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, n is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, n is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,n is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, p is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, p is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,p is 2.

In accordance with any one of the foregoing embodiments not otherwiseexcluded, in one embodiment, R¹⁰ is

n is 0, p is 0, each instance of R¹² is hydrogen, and R¹¹ is selectedfrom the group consisting of aryl and methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

n is 0, X′ is CH₂, and R″ is methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

In accordance with any one of the foregoing embodiments, in oneembodiment, R* is a chiral group

of at least 95% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment, R* is a chiral group

of at least 98% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment, R* is a chiral group

of at least 99% enantiomeric excess.

An aspect of the invention concerns a method of forming a compound offormula (II)

The method includes the step of reacting a compound represented byformula (IV)

with a compound of formula (V)

R¹⁰—B(OH)₂  (V),

wherein:

B in formula (II) is a boron atom having sp³ hybridization;

the carbon atom marked “*” is a chiral carbon atom of at least 90%enantiomeric excess;

R¹⁰ is selected from the group consisting of

-   -   R¹¹ and each instance of R¹² are independently selected from the        group consisting of hydrogen, halogen, hydroxyl, (C1-C10)alkyl,        cycloalkyl, aryl, aralkyl, heteroaralkyl, alkoxyl, acyl,        acyloxy, aryloxy, amino, and trialkylsilyloxy; or R¹¹ and any        one instance of R¹², or any two instances of R¹², taken        together, form a 3-10-membered ring;    -   X is halogen;    -   each instance of Z is independently selected from the group        consisting of CH and N, provided that no more than two instances        of Z are N;    -   X′ is selected from the group consisting of CR⁵R⁶, 0, S, and        NR⁷;    -   R¹ and R² are both hydrogen or identically selected        (C1-C3)alkyl;    -   R⁵ and R⁶ are independently selected from the group consisting        of hydrogen, halogen, hydroxyl, (C1-C10)alkyl, cycloalkyl, aryl,        aralkyl, heteroaralkyl, alkoxyl, acyl, acyloxy, aryloxy, amino,        and trialkylsilyloxy;    -   R⁷ and R³⁰ are independently selected from the group consisting        of hydrogen and (C1-C3)alkyl;    -   n is 0, 1, or 2;    -   p is 0, 1, or 2; and    -   q is 1 or 2.

In one embodiment, the compound of formula (II) is

In accordance with any one of the foregoing embodiments, in oneembodiment, R⁵ and R⁶ are independently selected from the groupconsisting of hydrogen and (C1-C3)alkyl.

In accordance with any one of the foregoing embodiments, in oneembodiment, n is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, n is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,n is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, p is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, p is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,p is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, q is 1. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, q is 2.

In accordance with any one of the foregoing embodiments not otherwiseexcluded, in one embodiment, R¹⁰ is

n is 0, p is 0, each instance of R¹² is hydrogen, and R¹¹ is selectedfrom the group consisting of aryl and methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

n is 0, X′ is CH₂, and R¹¹ is methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

In accordance with any one of the foregoing embodiments, in oneembodiment the carbon atom marked “*” is a chiral carbon atom of atleast 95% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment the carbon atom marked “*” is achiral carbon atom of at least 98% enantiomeric excess. In accordancewith any one of the foregoing embodiments, in one embodiment the carbonatom marked “*” is a chiral carbon atom of at least 99% enantiomericexcess.

The stereoisomerically enriched or substantially pure chiralorganoboronic acids of the invention are useful in performingstereoselective chemical reactions. In addition to the use of thestereoisomerically enriched or substantially pure chiral organoboronicacids of the invention, the stereoselective reactions can furtherinclude the use of one or more chiral reagents, thereby achieving atleast an additive effect in terms of the overall stereoselectivity ofthe reaction.

An aspect of the invention is a method of performing a stereoselectivechemical reaction. The method includes the step of contacting a compoundof formula (I) with a reagent

-   -   wherein:    -   R¹⁰ is chemically transformed in a stereoselective manner;    -   B is a boron atom having spa hybridization;    -   R* is a chiral group

of at least 90% enantiomeric excess;

-   -   R²¹ and R²² are independently selected from the group consisting        of hydrogen, alkyl, cycloalkyl, heterocyclyl, aryl, heteroaryl,        aralkyl, and heteroaralkyl; or R²¹ and R²², taken together, form        a 5-10-membered cycloalkyl or aromatic ring, or form a        5-10-membered heterocyclic or heteroaromatic ring comprising 1-3        heteroatoms independently selected from the group consisting of        N, O, and S;    -   R²³ is selected from the group consisting of hydrogen, alkyl,        cycloalkyl, heterocyclyl, aryl, heteroaryl, aralkyl, and        heteroaralkyl;    -   R¹⁰ is selected from the group consisting of

-   -   R¹¹ and each instance of R¹² are independently selected from the        group consisting of hydrogen, halogen, hydroxyl, (C1-C10)alkyl,        cycloalkyl, aryl, aralkyl, heteroaralkyl, alkoxyl, acyl,        acyloxy, aryloxy, amino, and trialkylsilyloxy; or and any one        instance of R¹², or any two instances of R¹², taken together,        form a 3-10-membered ring;    -   X is halogen;    -   each instance of Z is independently selected from the group        consisting of CH and N, provided that no more than two instances        of Z are N;    -   X′ is selected from the group consisting of CR⁵R⁶, O, S, and        NR′;    -   R¹ and R² are both hydrogen or identically selected        (C1-C3)alkyl;    -   R³ and R⁴ are both hydrogen or identically selected        (C1-C3)alkyl;    -   R⁵ and R⁶ are independently selected from the group consisting        of hydrogen, halogen, hydroxyl, (C1-C10)alkyl, cycloalkyl, aryl,        aralkyl, heteroaralkyl, alkoxyl, acyl, acyloxy, aryloxy, amino,        and trialkylsilyloxy;    -   R⁷ is selected from the group consisting of hydrogen and        (C1-C3)alkyl;    -   m is 0, 1, or 2;    -   n is 0, 1, or 2; and    -   p is 0, 1, or 2.

In an alternative embodiment, all else being the same, R¹ and R², and/orR³ and R⁴, are independently selected from the group consisting ofhydrogen and (C1-C3)alkyl.

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is selected from the group consisting of

In one embodiment, R* is selected from the group consisting of

In one embodiment, R* is selected from the group consisting of

In one embodiment, R²¹ and R²², taken together, form a 5-10-memberedcycloalkyl or aromatic ring, or form a 5-10-membered heterocyclic orheteroaromatic ring comprising 1-3 heteroatoms independently selectedfrom the group consisting of N, O, and S.

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In accordance with any one of the foregoing embodiments, in oneembodiment, R⁵ and R⁶ are independently selected from the groupconsisting of hydrogen and (C1-C3)alkyl.

In accordance with any one of the foregoing embodiments, in oneembodiment, m is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, m is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,m is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, n is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, n is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,n is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, p is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, p is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,p is 2.

In accordance with any one of the foregoing embodiments not otherwiseexcluded, in one embodiment, R¹⁰ is

n is 0, p is 0, each instance of R¹² is hydrogen, and R^(H) is selectedfrom the group consisting of aryl and methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

n is 0, X′ is CH₂, and R¹¹ is methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

In accordance with any one of the foregoing embodiments, in oneembodiment, R* is a chiral group

of at least 95% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment, R* is a chiral group

of at least 98% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment, R* is a chiral group

of at least 99% enantiomeric excess.

In accordance with any one of the foregoing embodiments, in oneembodiment, the reagent is selected from the group consisting ofoxidants, nucleophiles, bases, and electrophiles.

In accordance with any one of the foregoing embodiments, in oneembodiment, reagent is meta-chloroperbenzoic acid (mCPBA).

In accordance with any one of the foregoing embodiments, in oneembodiment, the chemical reaction is selected from epoxidation,nucleophilic substitution, electrophilic substitution, oxidation,dihydroxylation, carbonylation, alkenation, cyclopropanation,cycloaddition, conjugate addition, Michael addition, Diels-Alderreaction, and transition metal-catalyzed cross-coupling reaction.

In accordance with any one of the foregoing embodiments, in oneembodiment, the transition metal-catalyzed cross-coupling reaction is aSuzuki-Miyaura reaction.

In accordance with any one of the foregoing embodiments, in oneembodiment, the chemical reaction is epoxidation.

In accordance with any one of the foregoing embodiments, in oneembodiment, the epoxidation is selected from the group consisting ofSharpless epoxidation and Jacobsen epoxidation.

In accordance with any one of the foregoing embodiments, in oneembodiment, the reagent is a chiral reagent.

In accordance with any one of the foregoing embodiments, in oneembodiment, the reagent is an achiral reagent.

An aspect of the invention is a method of performing a stereoselectivechemical reaction. The method includes the step of contacting a compoundof formula (II) with a reagent

wherein:

R¹⁰ is chemically transformed in a stereoselective manner;

the carbon atom marked “*” is a chiral carbon atom of at least 90%enantiomeric excess;

B is a boron atom having sp³ hybridization;

R¹⁰ is selected from the group consisting of

-   -   R¹¹ and each instance of R¹² are independently selected from the        group consisting of hydrogen, halogen, hydroxyl, (C1-C10)alkyl,        cycloalkyl, aryl, aralkyl, heteroaralkyl, alkoxyl, acyl,        acyloxy, aryloxy, amino, and trialkylsilyloxy; or R¹¹ and any        one instance of R¹², or any two instances of R¹², taken        together, form a 3-10-membered ring;    -   X is halogen;    -   each instance of Z is independently selected from the group        consisting of CH and N, provided that no more than two instances        of Z are N;    -   X′ is selected from the group consisting of CR⁵R⁶, O, S, and        NR⁷;    -   R¹ and R² are both hydrogen or identically selected        (C1-C3)alkyl;    -   R⁵ and R⁶ are independently selected from the group consisting        of hydrogen, halogen, hydroxyl, (C1-C10)alkyl, cycloalkyl, aryl,        aralkyl, heteroaralkyl, alkoxyl, acyl, acyloxy, aryloxy, amino,        and trialkylsilyloxy;    -   R⁷ and RN are independently selected from the group consisting        of hydrogen and (C1-C3)alkyl;    -   n is 0, 1, or 2;    -   p is 0, 1, or 2; and    -   q is 1 or 2.

In an alternative embodiment, all else being the same, R¹ and R² areindependently selected from the group consisting of hydrogen and(C1-C3)alkyl.

In one embodiment, the compound of formula (II) is

In accordance with any one of the foregoing embodiments, in oneembodiment, R⁵ and R⁶ are independently selected from the groupconsisting of hydrogen and (C1-C3)alkyl.

In accordance with any one of the foregoing embodiments, in oneembodiment, n is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, n is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,n is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, p is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, p is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,p is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, q is 1. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, q is 2.

In accordance with any one of the foregoing embodiments not otherwiseexcluded, in one embodiment, R¹⁰ is

n is 0, p is 0, each instance of R¹² is hydrogen, and R^(H) is selectedfrom the group consisting of aryl and methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

n is 0, X′ is CH₂, and R¹¹ is methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

In accordance with any one of the foregoing embodiments, in oneembodiment the carbon atom marked “*” is a chiral carbon atom of atleast 95% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment the carbon atom marked “*” is achiral carbon atom of at least 98% enantiomeric excess. In accordancewith any one of the foregoing embodiments, in one embodiment the carbonatom marked “*” is a chiral carbon atom of at least 99% enantiomericexcess.

In accordance with any one of the foregoing embodiments, in oneembodiment, the reagent is selected from the group consisting ofoxidants, nucleophiles, bases, and electrophiles.

In accordance with any one of the foregoing embodiments, in oneembodiment, reagent is meta-chloroperbenzoic acid (mCPBA).

In accordance with any one of the foregoing embodiments, in oneembodiment, the chemical reaction is selected from epoxidation,nucleophilic substitution, electrophilic substitution, oxidation,dihydroxylation, carbonylation, alkenation, cyclopropanation,cycloaddition, conjugate addition, Michael addition, Diels-Alderreaction, and transition metal-catalyzed cross-coupling reaction.

In accordance with any one of the foregoing embodiments, in oneembodiment, the transition metal-catalyzed cross-coupling reaction is aSuzuki-Miyaura reaction.

In accordance with any one of the foregoing embodiments, in oneembodiment, the chemical reaction is epoxidation.

In accordance with any one of the foregoing embodiments, in oneembodiment, the epoxidation is selected from the group consisting ofSharpless epoxidation and Jacobsen epoxidation.

In accordance with any one of the foregoing embodiments, in oneembodiment, the reagent is a chiral reagent.

In accordance with any one of the foregoing embodiments, in oneembodiment, the reagent is an achiral reagent.

Similar to protected organoboronic acids including a MIDA boronate esterprotecting group, stereoisomerically enriched or substantially purechiral organoboronic acids of the present invention are readily purifiedby column chromatography. This is unusual for boronic acids, which aretypically unstable to chromatographic techniques. These compounds alsomay be highly crystalline, which facilitates purification, utilization,and storage. These compounds are extremely stable to long term storage,including storage on the bench top under air. This is also unusual, asmany boronic acids are unstable to long term storage.

Stereoisomerically enriched or substantially pure chiral organoboronicacids of the present invention are characterized in part byconformational rigidity of an organic protecting group. Conformationalrigidity of an organic protecting group bonded to a boron atom isdetermined by the following “conformational rigidity test”. A 10milligram (mg) sample of a compound including a boron atom and anorganic protecting group bonded to the boron is dissolved in dry d₆-DMSOand transferred to an NMR tube. The sample is then analyzed by ¹H NMR attemperatures ranging from 23° C. to at least 100° C., e.g., to 150° C.At each temperature, the sample shim is optimized and a ¹H NMR spectrumis obtained. If the protecting group is not conformationally rigid, thensplit peaks for a set of diastereotopic protons in the ¹H NMR spectrumobtained at 23° C. will coalesce into a single peak in the ¹H NMRspectrum obtained at 100° C. If the protecting group is conformationallyrigid, then split peaks for a set of diastereotopic protons in the ¹HNMR spectrum obtained at 23° C. will remain split and will not coalesceinto a single peak in the ¹H NMR spectrum obtained at 100° C.

Similar to the MIDA boronate compounds disclosed in US 2009/0030238,stereoisomerically enriched or substantially pure chiral organoboronicacids of the present invention have a number of advantageous properties.The IDA group is typically effective in decreasing the reactivity of theboronic acid to which it is esterified. One possible explanation forthis decrease in reactivity is that a vacant, Lewis acidic boronp-orbital is not available to react with other substances. For example,the protected boron no longer has a vacant, Lewis acidic p-orbital tocomplex with the palladium catalyst involved in the Suzuki-Miyauratransformation. Thus, this protection strategy should decrease thereactivity of any boronic acid, including its reactivity toward theSuzuki-Miyaura transformation. In addition, the IDA boronate ester groupseems to be stable to a wide variety of reaction conditions, besidescross-coupling. This stability may facilitate their utilization in thesynthesis of complex synthetic building blocks that contain boronic acidfunctional groups.

Although these sp³-hybridized boronate esters having a conformationallyrigid protecting group bonded to the boron are protected from anhydrousSuzuki-Miyaura coupling even at 80° C. for 28 hours, deprotection can bereadily achieved at 23° C. using extremely mild aqueous basicconditions. One example of deprotection conditions is treatment with 1molar (M) aqueous sodium hydroxide (NaOH) in tetrahydrofuan (THF) for 10minutes. Another example of deprotection conditions is treatment withsaturated aqueous sodium bicarbonate (NaHCO₃) in methanol (MeOH) for 6hours. These mild conditions are in contrast to typical protectinggroups based on boronate esters, which can require harsh cleavageconditions.

Stereoisomerically enriched or substantially pure chiral organoboronicacids including a boron atom having sp³ hybridization, aconformationally rigid protecting group bonded to the boron atom, and anorganic group may be useful as synthetic building blocks. Examples ofbuilding blocks include protected haloorganoboronic acids. Furtherexamples of building blocks include bis-boronates having a first boronatom having sp³ hybridization and a conformationally rigid protectinggroup bonded to the first boron atom, and a second boron atom that maybe present as a boronic acid or as a different type of protected boron.The protecting group in each of these building blocks is represented asthe IDA boronate ester. Protected organoboronic acid building blocks mayalso include compounds having one or more substituent groups on theprotecting group, and/or having a different group bonded to the nitrogenof the protecting group. For example, the protecting groups in thesebuilding blocks may be a protecting group as described for formula (I)or for formula (II).

These reactions demonstrate some of the possible applications ofprotected organoboronic acids that include a boron having spahybridization and having a conformationally rigid protecting groupbonded to the boron. These compounds may be used for simple, highlymodular syntheses of molecules through iterative Suzuki-Miyauracross-coupling transformations. These transformations may involvebifunctional building blocks, such as protected organoboronic acids thatinclude a halogen or a pseudohalogen group. For a given synthesis, allthe building blocks may be prepared having the required functionalgroups preinstalled in the correct oxidation state and with the desiredstereochemical relationships. These building blocks may then be broughttogether by the recursive application of one mild reaction, such as theSuzuki-Miyaura reaction. In addition to being very simple, efficient,and potentially amenable to automation, this strategy is inherentlymodular and thus well-suited for making collections of structuralderivatives.

The synthesis of polyenes is made challenging by the sensitivity ofconjugated double bond frameworks to many common synthetic reagents.Controlling the geometry of each double bond is also a critical issue.Many valuable methods have been developed, but synthetic strategiesbased on palladium-mediated cross-coupling are particularly attractivedue to the mild and stereospecific nature of these reactions. In thisvein, a variety of methods based on bis-metallated (Lhermitte et al.(1996) Synlett 377-9; Lipshutz et al. (1997) J Am Chem Soc 119:4555-6;Pihko et al. (1999) Synlett 12:1966-8; Babudri et al. (1998) Tetrahedron54:1085-94; Murakami et al. (2004) Synthesis 9:1522-6; Denmark (2005) JAm Chem Soc 127:8004-5; Lipshutz et al. (2005) Org Chem Lett 7:4561-4;Coleman et al. (2005) Org Lett 7:2289-91; Coleman et al. (2007) J AmChem Soc 129:3826-7) or bis-halogenated (Organ et al. (2000) J Org Chem65:7959-70; Antunes et al. (2003) Tetrahedron Lett 44:6805-8; Organ etal. (2004) Tetrahedron 60:9453-61) lynchpin reagents have been reported.In these approaches, three fragments are brought together using twocross-coupling reactions to engage the orthogonally-reactive termini ofthe lynchpin.

An important advantage of the iterative cross-coupling strategy usingprotected organoboronic acids including a boron atom having spahybridization and having a conformationally rigid protecting groupbonded to the boron atom is the inherent potential for limitlessiteration. That is, all of the required building blocks can in theory bebrought together via the recursive application of a single, mildreaction. This may dramatically simplify the synthesis process, and mayreadily enable analog preparation. The use of only one reaction also canhelp to minimize the potential for incompatibilities between thefunctional groups appended to the building blocks and the reactionconditions used to couple them. In addition, the use of bifunctionalhaloorganoboronic acids can avoid toxic metals such as organostannes,which are frequently employed in bis-metallated lynchpin-type reagents.Finally, the protected haloorganoboronic acids tend to be free-flowingcrystalline solids that can be readily purified by silica gelchromatography and/or recrystallization and stored indefinitely on thebenchtop under air.

Bifunctional PIDA-Protected Haloboronic Acids

A key to the development of apparatuses and methods for the automatedsynthesis of small molecules was the use of the Suzuki-Miyaura reactionto achieve the iterative cross-coupling (ICC) of bifunctional“haloboronic acids”. However, in order to have an efficient automatableprocedure, the development of a mild and selective method for reversiblyattenuating one end of each haloboronic acid was required to avoidrandom oligomerization. In this vein, the apparatuses and methodsdescribed herein take advantage of the finding that the trivalent ligandN-pinene-derived iminodiacetic acid (PIDA), similar toN-methyliminodiacetic acid (MIDA), can act as a switch to turn thereactivity of a boronic acid “off” and “on” under very mild conditions(E. P. Gillis, M. D. Burke J. Am. Chem. Soc. 2007, 129, 6716-6717; andU.S. Patent Application Publication No. 2009/0030238, which isincorporated herein by reference in its entirety). This property of MIDAboronates has made it possible to prepare a variety of natural productsvia repeated cycles involving MIDA boronate deprotection, selectivecross-coupling, and purification (S. J. Lee, K. C. Gray, J. S. Paek, M.D. Burke J. Am. Chem. Soc. 2008, 130, 466-468; E. P. Gillis, M. D.Burke, J. Am. Chem. Soc. 2008, 130, 14084-14085; and E. M. Woerly, A. H.Cherney, E. K. Davis, M. D. Burke, J. Am. Chem. Soc. 2010, 132,6941-6943). Further enabling their general utility as building blocks,PIDA boronates are uniformly air-stable, highly crystalline, monomeric,free-flowing solids that are fully compatible with a wide range ofcommon synthetic reagents and silica gel chromatography.

Purification of PIDA-Protected Organoboronic Acids

Transforming an ICC approach into a fully automated process requires ageneral strategy for purifying the synthetic intermediates. In the caseof peptides, oligonucleotides, and oligosaccharides this problem hasbeen solved by linking the growing oligomer to a solid support. At theend of each coupling reaction, the desired product is separated fromresidual solvents, reagents, and byproducts via a simple filtration.Albeit highly effective in these contexts, there are two majorlimitations of this purification approach as a foundation for ICC-basedsmall molecule synthesis.

First, this strategy requires a ubiquitous chemical handle that enablescovalent linking of the growing oligomer to the solid phase. In the caseof peptides, oligonucleotides, and oligosaccharides, the respectivemonomers all conveniently contain a common heteroatom linking element asan inherent component of the targeted structure. In contrast, althoughsome excellent solid-phase linking systems have been developed, smallmolecules are quite structurally diverse, and many lack a commonfunctional group available for attachment to a solid phase.

Second, selectively coupling boronic acids in the presence of PIDAboronates requires that relatively anhydrous conditions be utilizedbecause PIDA boronates are stable and unreactive under anhydrous basicconditions, but are readily hydrolyzed to yield reactive boronic acidswhen treated with aqueous base. In preliminary studies, it was foundthat translating the chemistry of anhydrous Suzuki-Miyauracross-couplings to the solid-phase can be problematic.

Surprisingly, the inventors have discovered two remarkable physicalproperties of PIDA boronates, allowing the circumvention of both of theaforementioned challenges. Collectively, the two properties have enableda highly effective alternative purification strategy and, thus, allowedthe complete automation of ICC with solution-phase chemistry. The twopurification strategies—“precipitation” and “catch-and-release”—arediscussed in detail below. The two purification strategies can be usedalone or in combination, in which case they may be performedsequentially in either order.

Purification by Precipitation. One aspect of the invention relates tothe discovery that virtually all molecules containing a PIDA-protectedorganoboronic acid functional group are insoluble in hexanes:THF (3:1v/v), while almost all boronic acids, other boronic esters, or relatedsurrogates are soluble in this solvent system. This general physicalproperty of PIDA boronates enables a highly efficientprecipitation-based purification. (For background on precipitation-basedpurification see: H. Perrier, M. Labelle, J. Org. Chem. 1999, 64,2110-2113; T. Bosanac, C. S. Wilcox, Org. Lett. 2004, 6, 2321-2324; andJ. C. Poupon, A. A. Boezio, A. B. Charette, Angew. Chem. Int. Ed. 2006,45, 1415-1420). Further, because most catalyst species and organichalides are soluble in hexanes:THF (3:1), PIDA boronates can be directlypurified from cross-coupling reactions, such as anhydrous Suzukicross-coupling reactions. Merely transferring a crude product mixture inTHF (e.g., from a cross-coupling reaction) to a stirred vesselcontaining an amount of hexanes which is approximately three times thetotal volume of THF to be added results in rapid and quantitativeprecipitation of the chiral, non-racemic PIDA boronate product while theresidual unreacted boronic acid, as well as most byproducts and otherreaction components, such as palladium and phosphine ligands, all remainsoluble in the hexane:THF (3:1 v/v) mixture. Simple filtration of thismixture, followed by dissolution of the precipitated chiral, non-racemicPIDA boronate with THF, yields a solution of semi-purified PIDAboronate.

One aspect of the invention relates to a method of purifying a chiral,non-racemic PIDA boronate from a solution, comprising the steps ofdiluting with hexane the solution comprising the PIDA boronate, therebyselectively precipitating the PIDA boronate; and isolating theprecipitated PIDA boronate. The hexane can be any isomer of hexane or amixture of hexanes. Exemplary isomers of hexane useful in the inventioninclude unbranched hexane (n-hexane), branched hexanes (e.g.,isohexane), and cyclohexane.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the precipitated chiral, non-racemicPIDA boronate is isolated by filtration.

In certain embodiments, the present invention relates to any one of theaforementioned methods, further comprising the step of dissolving theprecipitated chiral, non-racemic PIDA boronate in a polar solvent. Incertain embodiments, the present invention relates to any one of theaforementioned methods, further comprising the step of dissolving theprecipitated chiral, non-racemic PIDA boronate in THF.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the solution comprising the chiral,non-racemic PIDA boronate is a THF solution.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the solution comprising the chiral,non-racemic PIDA boronate is added dropwise to the hexane.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the volume of hexane is between abouttwo and about four times the volume of the solution comprising the PIDAboronate.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the volume of hexane is about threetimes the volume of the solution comprising the PIDA boronate.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the solution comprising the chiral,non-racemic PIDA boronate is a crude product mixture from a chemicalreaction.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chemical reaction is selected fromthe group consisting of a Suzuki-Miyaura coupling, an oxidation, a Swernoxidation, a “Jones reagents” oxidation, a reduction, an Evans' aldolreaction, an HWE olefination, a Takai olefination, an alcoholsilylation, a desilylation, a p-methoxybenzylation, an iodination, aNegishi cross-coupling, a Heck coupling, a Miyaura borylation, a Stillecoupling, and a Sonogashira coupling.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chemical reaction is selected fromepoxidation, nucleophilic substitution, electrophilic substitution,oxidation, dihydroxylation, carbonylation, alkenation, cyclopropanation,cycloaddition, conjugate addition, Michael addition, Diels-Alderreaction, and transition metal-catalyzed cross-coupling reaction.

In accordance with any one of the foregoing embodiments, in oneembodiment, the transition metal-catalyzed cross-coupling reaction is aSuzuki-Miyaura reaction.

In accordance with any one of the foregoing embodiments, in oneembodiment, the chemical reaction is epoxidation.

In accordance with any one of the foregoing embodiments, in oneembodiment, the epoxidation is selected from the group consisting ofSharpless epoxidation and Jacobsen epoxidation.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chemical reaction comprises the stepof contacting a chiral, non-racemic PIDA boronate with a reagent,wherein the chiral, non-racemic PIDA boronate comprises a boron havingan sp³ hybridization, a PIDA protecting group bonded to the boron, andan organic group bonded to the boron through a boron-carbon bond; theorganic group is chemically transformed, and the boron is not chemicallytransformed.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chiral, non-racemic PIDA boronate isrepresented by

-   -   wherein:    -   B is a boron atom having sp³ hybridization;    -   R* is a chiral group

of at least 90% enantiomeric excess;

-   -   R²¹ and R²² are independently selected from the group consisting        of hydrogen, alkyl, cycloalkyl, heterocyclyl, aryl, heteroaryl,        aralkyl, and heteroaralkyl; or R²¹ and R²², taken together, form        a 5-10-membered cycloalkyl or aromatic ring, or form a        5-10-membered heterocyclic or heteroaromatic ring comprising 1-3        heteroatoms independently selected from the group consisting of        N, O, and S;    -   R²³ is selected from the group consisting of hydrogen, alkyl,        cycloalkyl, heterocyclyl, aryl, heteroaryl, aralkyl, and        heteroaralkyl;    -   R¹⁰ is selected from the group consisting of

-   -   R¹¹ and each instance of R¹² are independently selected from the        group consisting of hydrogen, halogen, hydroxyl, (C1-C10)alkyl,        cycloalkyl, aryl, aralkyl, heteroaralkyl, alkoxyl, acyl,        acyloxy, aryloxy, amino, and trialkylsilyloxy; or R¹¹ and any        one instance of R¹², or any two instances of R¹², taken        together, form a 3-10-membered ring;    -   X is halogen;    -   each instance of Z is independently selected from the group        consisting of CH and N, provided that no more than two instances        of Z are N;    -   X′ is selected from the group consisting of CR⁵R⁶, O, S, and        NR′;    -   R¹ and R² are both hydrogen or identically selected        (C1-C3)alkyl;    -   R³ and R⁴ are both hydrogen or identically selected        (C1-C3)alkyl;    -   R⁵ and R⁶ are independently selected from the group consisting        of hydrogen, halogen, hydroxyl, (C1-C10)alkyl, cycloalkyl, aryl,        aralkyl, heteroaralkyl, alkoxyl, acyl, acyloxy, aryloxy, amino,        and trialkylsilyloxy;    -   R⁷ is selected from the group consisting of hydrogen and        (C1-C3)alkyl;    -   m is 0, 1, or 2;    -   n is 0, 1, or 2; and    -   p is 0, 1, or 2.

In an alternative embodiment, all else being the same, R¹ and R², and/orR³ and R⁴, are independently selected from the group consisting ofhydrogen and (C1-C3)alkyl.

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is selected from the group consisting of

In one embodiment, R* is selected from the group consisting of

In one embodiment, R* is selected from the group consisting of

In one embodiment, R²¹ and R²², taken together, form a 5-10-memberedcycloalkyl or aromatic ring, or form a 5-10-membered heterocyclic orheteroaromatic ring comprising 1-3 heteroatoms independently selectedfrom the group consisting of N, O, and S.

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In accordance with any one of the foregoing embodiments, in oneembodiment, R⁵ and R⁶ are independently selected from the groupconsisting of hydrogen and (C1-C3)alkyl.

In accordance with any one of the foregoing embodiments, in oneembodiment, m is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, m is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,m is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, n is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, n is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,n is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, p is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, p is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,p is 2.

In accordance with any one of the foregoing embodiments not otherwiseexcluded, in one embodiment, R¹⁰ is

n is 0, p is 0, each instance of R¹² is hydrogen, and R^(H) is selectedfrom the group consisting of aryl and methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

n is O, X′ is CH₂, and R¹¹ is methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

In accordance with any one of the foregoing embodiments, in oneembodiment, R* is a chiral group

of at least 95% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment, R* is a chiral group

of at least 98% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment, R* is a chiral group

of at least 99% enantiomeric excess.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chiral, non-racemic PIDA boronate isrepresented by

wherein:

B is a boron atom having sp³ hybridization;

the carbon atom marked “*” is a chiral carbon atom of at least 90%enantiomeric excess;

-   -   R¹⁰ is selected from the group consisting of

-   -   R¹¹ and each instance of R¹² are independently selected from the        group consisting of hydrogen, halogen, hydroxyl, (C1-C10)alkyl,        cycloalkyl, aryl, aralkyl, heteroaralkyl, alkoxyl, acyl,        acyloxy, aryloxy, amino, and trialkylsilyloxy; or R¹¹ and any        one instance of R¹², or any two instances of R¹², taken        together, form a 3-10-membered ring;    -   X is halogen;    -   each instance of Z is independently selected from the group        consisting of CH and N, provided that no more than two instances        of Z are N;    -   X′ is selected from the group consisting of CR⁵R⁶, O, S, and        NR⁷;    -   R¹ and R² are both hydrogen or identically selected        (C1-C3)alkyl;    -   R⁵ and R⁶ are independently selected from the group consisting        of hydrogen, halogen, hydroxyl, (C1-C10)alkyl, cycloalkyl, aryl,        aralkyl, heteroaralkyl, alkoxyl, acyl, acyloxy, aryloxy, amino,        and trialkylsilyloxy;    -   R⁷ and RN are independently selected from the group consisting        of hydrogen and (C1-C3)alkyl;    -   n is 0, 1, or 2;    -   p is 0, 1, or 2; and    -   q is 1 or 2.

In an alternative embodiment, all else being the same, R¹ and R² areindependently selected from the group consisting of hydrogen and(C1-C3)alkyl.

In one embodiment, the compound of formula (II) is

In accordance with any one of the foregoing embodiments, in oneembodiment, n is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, n is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,n is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, p is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, p is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,p is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, q is 1. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, q is 2.

In accordance with any one of the foregoing embodiments not otherwiseexcluded, in one embodiment, R¹⁰ is

n is 0, p is 0, each instance of R¹² is hydrogen, and R^(H) is selectedfrom the group consisting of aryl and methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

n is O, X′ is CH₂, and R¹¹ is methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

In accordance with any one of the foregoing embodiments, in oneembodiment the carbon atom marked “*” is a chiral carbon atom of atleast 95% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment the carbon atom marked “*” is achiral carbon atom of at least 98% enantiomeric excess. In accordancewith any one of the foregoing embodiments, in one embodiment the carbonatom marked “*” is a chiral carbon atom of at least 99% enantiomericexcess.

Catch-and-Release Purification. It has further been found that allmolecules which contain a chiral, non-racemic PIDA boronate functionalgroup have exceptionally high affinity for silica gel. For example, ithas been discovered that PIDA boronates, regardless of the nature of theorganic group appended to boron, have an R_(f) of essentially zero inhexanes:THF (3:1 v/v), Et₂O, and Et₂O:MeOH (98.5:1.5 v/v). Therefore,PIDA boronates can be used as a universal tag for catch-and-releasepurification on silica gel. (For an excellent review on taggingstrategies for separations in organic synthesis, see: J. Yoshida, K.Itami, Chem. Rev. 2002, 102, 3693-3716. For an excellent review onmodern separation techniques in organic synthesis, see: C. C. Tzschucke,C. Markert, W. Bannwarth, S. Roller, A. Hebel, R. Haag, Angew. Chem.Int. Ed. 2002, 41, 3964-4000. See, also, D. P. Curran, Angew. Chem. Int.Ed. 1998, 37, 1174-1196; P. H. Toy, K. D. Janda, Acc. Chem. Res. 2000,33, 546-554; S. V. Ley, A. Massi, F. Rodriguez, D. C. Horwell, R. A.Lewthwaite, M. C. Pritchard, A. M. Reid, Angew. Chem. Int. Ed. 2001, 40,1053-1055; A. R. Brown, S. L. Irving, R. Ramage, G. Raphy Tetrahedron1995, 51, 11815-11830; L. A. Thompson, Curr. Opin. Chem. Bio. 2000, 4,324-337; and M. G. Siegel, P. J. Hahn, B. A. Dressman, J. E. Fritz, J.R. Grunwell, S. W. Kaldor, Tetrahedron Lett. 1997, 38, 3357-3360. Forthe use of catch-and-release type methods to purify proteins, see: J.Porath, J. Carlsson, I. Olsson, G. Belfrage, Nature 1975, 278, 598.) Inother words, the chiral, non-racemic PIDA boronate functional group,which is conveniently present in all intermediates utilized in certainICC sequences, enables the reversible non-covalent attachment of anychiral, non-racemic PIDA boronate to silica gel, a solid support.

The use of hexanes:THF (e.g., 3:1 v/v) as a solvent system is importantsince it provides a means (via diluting with hexanes) to purify directlyTHF reaction solutions containing PIDA boronates. With regards toautomated synthesis, as discussed below, this feature is importantbecause advanced manipulations, such as solvent evaporation, are notrequired to prepare the reaction solution for purification. The use ofEt₂O is important because in certain coupling reactions almost everyother compound present in the reaction solution elutes in Et₂O.Interestingly, the addition of 1.5% MeOH (v/v) to the Et₂O ensures thateven polar boronic acids are eluted off of the column with a reasonableamount of solvent. The compatibility of MeOH with PIDA boronates in thepurification method was unexpected since MeOH can be used to deprotectPIDA boronates to the corresponding boronic acid at room temperature.All of the above-mentioned properties have been tested with many PIDAboronates and have been shown to be general. Once the unreacted boronicacids, as well as reaction regents, have been eluted, pure PIDAboronates generally elute well in THF. Also, PIDA boronates generallyelute well with MeCN and acetone.

One aspect of the invention relates to a method of purifying a chiral,non-racemic PIDA boronate from a solution, comprising the steps ofpassing the solution through a silica plug; passing a first liquidthrough the silica plug; and passing a second liquid through the silicaplug, thereby eluting the chiral, non-racemic PIDA boronate in thesecond liquid; wherein the first liquid contains diethyl ether or thepolarity of the first liquid is less than or equal to about the polarityof a mixture of 98.5:1.5 (v/v) Et₂O:MeOH; and the polarity of the secondliquid is greater than or equal to about the polarity of THF.

PIDA boronates, like most organic compounds, generally elute morerapidly off of SiO₂ (i.e., have a higher R_(f)) when the polarity of thesolvent is higher. However, the purification method described abovetakes advantage of special properties of PIDA boronates in certainsolvents. Specifically, there are certain solvent systems in which theR_(f) of a chiral, non-racemic PIDA boronate is not related to thepolarity of the solvent. In fact, in certain solvent systems the R_(f)can approach or be zero. For example, even though chloroform is morepolar than THF, the R_(f) of dodecyl chiral, non-racemic PIDA boronatein chloroform is 0.00 and in THF is 0.80. While not intending to bebound by any particular theory, this very surprising phenomenon likelyinvolves a unique interaction among all three factors: the solvent,silica gel, and PIDA boronate. Thus, it is possible to isolate a chiral,non-racemic PIDA boronate on a silica column if one picks a solvent thatis an exception to the elution rules (such as chloroform or Et₂O). Toremove a chiral, non-racemic PIDA boronate from the column thus loaded,one switches to a polar solvent that obeys the normal elution rules(such as THF, MeCN, or acetone).

It has also been found that a functionalized silica gel, such as3-aminopropyl-functionalized silica gel, can be substituted for SiO₂without affecting the properties of the PIDA boronate/SiO₂ interaction.The functionalized silica gel can be used to scavenge, for example,metal catalysts from the solution. Therefore, in certain embodiments,the present invention relates to any one of the aforementioned methods,wherein the silica is 3-aminopropyl-functionalized silica.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the first liquid comprises diethylether.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the first liquid is diethyl ether.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the first liquid is a mixture of diethylether and methanol.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein first liquid is a mixture of diethylether and methanol; and the ratio of diethyl ether to methanol is98.5:1.5 (v/v).

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the second liquid is THF, MeCN, ethylacetate or acetone, or a solvent of similar polarity.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the second liquid is THF, MeCN, ethylacetate or acetone.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the second liquid is THF.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the solution is a crude product mixturefrom a chemical reaction.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chemical reaction is selected fromthe group consisting of a Suzuki-Miyaura coupling, an oxidation, a Swernoxidation, a “Jones reagents” oxidation, a reduction, an Evans' aldolreaction, an HWE olefination, a Takai olefination, an alcoholsilylation, a desilylation, a p-methoxybenzylation, an iodination, aNegishi cross-coupling, a Heck coupling, a Miyaura borylation, a Stillecoupling, and a Sonogashira coupling.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chemical reaction is selected fromepoxidation, nucleophilic substitution, electrophilic substitution,oxidation, dihydroxylation, carbonylation, alkenation, cyclopropanation,cycloaddition, conjugate addition, Michael addition, Diels-Alderreaction, and transition metal-catalyzed cross-coupling reaction.

In accordance with any one of the foregoing embodiments, in oneembodiment, the transition metal-catalyzed cross-coupling reaction is aSuzuki-Miyaura reaction.

In accordance with any one of the foregoing embodiments, in oneembodiment, the chemical reaction is epoxidation.

In accordance with any one of the foregoing embodiments, in oneembodiment, the epoxidation is selected from the group consisting ofSharpless epoxidation and Jacobsen epoxidation.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chemical reaction comprises thesteps of contacting a chiral, non-racemic PIDA boronate with a reagent,wherein the chiral, non-racemic PIDA boronate comprises a boron havingan sp³ hybridization, a PIDA protecting group bonded to the boron, andan organic group bonded to the boron through a boron-carbon bond; theorganic group is chemically transformed, and the boron is not chemicallytransformed.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chiral, non-racemic PIDA boronate isrepresented by

-   -   wherein:    -   B is a boron atom having sp³ hybridization;    -   R* is a chiral group

of at least 90% enantiomeric excess;

-   -   R²¹ and R²² are independently selected from the group consisting        of hydrogen, alkyl, cycloalkyl, heterocyclyl, aryl, heteroaryl,        aralkyl, and heteroaralkyl; or R²¹ and R²², taken together, form        a 5-10-membered cycloalkyl or aromatic ring, or form a        5-10-membered heterocyclic or heteroaromatic ring comprising 1-3        heteroatoms independently selected from the group consisting of        N, O, and S;    -   R²³ is selected from the group consisting of hydrogen, alkyl,        cycloalkyl, heterocyclyl, aryl, heteroaryl, aralkyl, and        heteroaralkyl;    -   R¹⁰ is selected from the group consisting of

-   -   R¹¹ and each instance of R¹² are independently selected from the        group consisting of hydrogen, halogen, hydroxyl, (C1-C10)alkyl,        cycloalkyl, aryl, aralkyl, heteroaralkyl, alkoxyl, acyl,        acyloxy, aryloxy, amino, and trialkylsilyloxy; or R¹¹ and any        one instance of R¹², or any two instances of R¹², taken        together, form a 3-10-membered ring;    -   X is halogen;    -   each instance of Z is independently selected from the group        consisting of CH and N, provided that no more than two instances        of Z are N;    -   X′ is selected from the group consisting of CR⁵R⁶, O, S, and        NR⁷;    -   R¹ and R² are both hydrogen or identically selected        (C1-C3)alkyl;    -   R³ and R⁴ are both hydrogen or identically selected        (C1-C3)alkyl;    -   R⁵ and R⁶ are independently selected from the group consisting        of hydrogen, halogen, hydroxyl, (C1-C10)alkyl, cycloalkyl, aryl,        aralkyl, heteroaralkyl, alkoxyl, acyl, acyloxy, aryloxy, amino,        and trialkylsilyloxy;    -   R⁷ is selected from the group consisting of hydrogen and        (C1-C3)alkyl;    -   m is 0, 1, or 2;    -   n is 0, 1, or 2; and    -   p is 0, 1, or 2.

In an alternative embodiment, all else being the same, R¹ and R², and/orR³ and R⁴, are independently selected from the group consisting ofhydrogen and (C1-C3)alkyl.

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is selected from the group consisting of

In one embodiment, R* is selected from the group consisting of

In one embodiment, R* is selected from the group consisting of

In one embodiment, R²¹ and R²², taken together, form a 5-10-memberedcycloalkyl or aromatic ring, or form a 5-10-membered heterocyclic orheteroaromatic ring comprising 1-3 heteroatoms independently selectedfrom the group consisting of N, O, and S.

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In accordance with any one of the foregoing embodiments, in oneembodiment, R⁵ and R⁶ are independently selected from the groupconsisting of hydrogen and (C1-C3)alkyl.

In accordance with any one of the foregoing embodiments, in oneembodiment, m is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, m is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,m is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, n is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, n is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,n is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, p is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, p is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,p is 2.

In accordance with any one of the foregoing embodiments not otherwiseexcluded, in one embodiment, R¹⁰ is

n is 0, p is 0, each instance of R¹² is hydrogen, and R¹¹ is selectedfrom the group consisting of aryl and methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

n is O, X′ is CH₂, and R¹¹ is methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

In accordance with any one of the foregoing embodiments, in oneembodiment, R* is a chiral group

of at least 95% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment, R* is a chiral group

of at least 98% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment, R* is a chiral group

of at least 99% enantiomeric excess.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chiral, non-racemic PIDA boronate isrepresented by

wherein:

B is a boron atom having sp³ hybridization;

the carbon atom marked “*” is a chiral carbon atom of at least 90%enantiomeric excess;

-   -   R¹⁰ is selected from the group consisting of

-   -   R¹¹ and each instance of R¹² are independently selected from the        group consisting of hydrogen, halogen, hydroxyl, (C1-C10)alkyl,        cycloalkyl, aryl, aralkyl, heteroaralkyl, alkoxyl, acyl,        acyloxy, aryloxy, amino, and trialkylsilyloxy; or R¹¹ and any        one instance of R¹², or any two instances of R¹², taken        together, form a 3-10-membered ring;    -   X is halogen;    -   each instance of Z is independently selected from the group        consisting of CH and N, provided that no more than two instances        of Z are N;    -   X′ is selected from the group consisting of CR⁵R⁶, O, S, and        NR⁷;    -   R¹ and R² are both hydrogen or identically selected        (C1-C3)alkyl;    -   R⁵ and R⁶ are independently selected from the group consisting        of hydrogen, halogen, hydroxyl, (C1-C10)alkyl, cycloalkyl, aryl,        aralkyl, heteroaralkyl, alkoxyl, acyl, acyloxy, aryloxy, amino,        and trialkylsilyloxy;    -   R⁷ and R³⁰ are independently selected from the group consisting        of hydrogen and (C1-C3)alkyl;    -   n is 0, 1, or 2;    -   p is 0, 1, or 2; and    -   q is 1 or 2.

In an alternative embodiment, all else being the same, R¹ and R² areindependently selected from the group consisting of hydrogen and(C1-C3)alkyl.

In one embodiment, the compound of formula (II) is

In accordance with any one of the foregoing embodiments, in oneembodiment, n is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, n is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,n is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, p is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, p is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,p is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, q is 1. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, q is 2.

In accordance with any one of the foregoing embodiments not otherwiseexcluded, in one embodiment, R¹⁰ is

n is 0, p is 0, each instance of R¹² is hydrogen, and R¹¹ is selectedfrom the group consisting of aryl and methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

n is 0, X′ is CH₂, and R¹¹ is methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

In accordance with any one of the foregoing embodiments, in oneembodiment the carbon atom marked “*” is a chiral carbon atom of atleast 95% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment the carbon atom marked “*” is achiral carbon atom of at least 98% enantiomeric excess. In accordancewith any one of the foregoing embodiments, in one embodiment the carbonatom marked “*” is a chiral carbon atom of at least 99% enantiomericexcess.

Combination Precipitation & Catch-and-Release Purification. The twopurification strategies discussed above can be combined into one robustand general process. Specifically, the solution which is subjected tothe catch-and-release purification described above can be a solutionwhich is derived from the selective precipitation of a PIDA boronate.

One aspect of the invention relates to a method of purifying a chiral,non-racemic PIDA boronate from a solution, comprising the steps ofdiluting the solution with hexane, thereby selectively precipitating thePIDA boronate; passing the diluted solution through a silica plug,thereby depositing the precipitated PIDA-protected organoboronic acid onthe silica plug; passing a first liquid through the silica plug; andpassing a second liquid through the silica plug, thereby eluting thechiral, non-racemic PIDA boronate in the second liquid; wherein thefirst liquid contains diethyl ether or the polarity of the first liquidis less than or equal to about the polarity of a mixture of 98.5:1.5(v/v) Et₂O:MeOH; and the polarity of the second liquid is greater thanor equal to about the polarity of THF.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the first liquid comprises diethylether.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the first liquid is diethyl ether.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the first liquid is a mixture of diethylether and methanol.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein first liquid is a mixture of diethylether and methanol; and the ratio of diethyl ether to methanol is98.5:1.5 (v/v).

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the second liquid is THF, MeCN, ethylacetate or acetone, or a solvent of similar or greater polarity.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the second liquid is THF, MeCN, ethylacetate or acetone.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the second liquid is THF.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the solution is a crude product mixturefrom a chemical reaction.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chemical reaction is selected fromthe group consisting of a Suzuki-Miyaura coupling, an oxidation, a Swernoxidation, a “Jones reagents” oxidation, a reduction, an Evans' aldolreaction, an HWE olefination, a Takai olefination, an alcoholsilylation, a desilylation, a p-methoxybenzylation, an iodination, aNegishi cross-coupling, a Heck coupling, a Miyaura borylation, a Stillecoupling, and a Sonogashira coupling.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chemical reaction is selected fromepoxidation, nucleophilic substitution, electrophilic substitution,oxidation, dihydroxylation, carbonylation, alkenation, cyclopropanation,cycloaddition, conjugate addition, Michael addition, Diels-Alderreaction, and transition metal-catalyzed cross-coupling reaction.

In accordance with any one of the foregoing embodiments, in oneembodiment, the transition metal-catalyzed cross-coupling reaction is aSuzuki-Miyaura reaction.

In accordance with any one of the foregoing embodiments, in oneembodiment, the chemical reaction is epoxidation.

In accordance with any one of the foregoing embodiments, in oneembodiment, the epoxidation is selected from the group consisting ofSharpless epoxidation and Jacobsen epoxidation.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chemical reaction comprises thesteps of contacting a chiral, non-racemic PIDA boronate with a reagent,wherein the chiral, non-racemic PIDA boronate comprises a boron havingan sp³ hybridization, a PIDA protecting group bonded to the boron, andan organic group bonded to the boron through a boron-carbon bond; theorganic group is chemically transformed, and the boron is not chemicallytransformed.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chiral, non-racemic PIDA boronate isrepresented by

-   -   wherein:    -   B is a boron atom having sp³ hybridization;    -   R* is a chiral group

of at least 90% enantiomeric excess;

-   -   R²¹ and R²² are independently selected from the group consisting        of hydrogen, alkyl, cycloalkyl, heterocyclyl, aryl, heteroaryl,        aralkyl, and heteroaralkyl; or R²¹ and R²², taken together, form        a 5-10-membered cycloalkyl or aromatic ring, or form a        5-10-membered heterocyclic or heteroaromatic ring comprising 1-3        heteroatoms independently selected from the group consisting of        N, O, and S;    -   R²³ is selected from the group consisting of hydrogen, alkyl,        cycloalkyl, heterocyclyl, aryl, heteroaryl, aralkyl, and        heteroaralkyl;    -   R¹⁰ is selected from the group consisting of

-   -   R¹¹ and each instance of R¹² are independently selected from the        group consisting of hydrogen, halogen, hydroxyl, (C1-C10)alkyl,        cycloalkyl, aryl, aralkyl, heteroaralkyl, alkoxyl, acyl,        acyloxy, aryloxy, amino, and trialkylsilyloxy; or R^(H) and any        one instance of R¹², or any two instances of R¹², taken        together, form a 3-10-membered ring;    -   X is halogen;    -   each instance of Z is independently selected from the group        consisting of CH and N, provided that no more than two instances        of Z are N;    -   X′ is selected from the group consisting of CR⁵R⁶, O, S, and        NR⁷;    -   R¹ and R² are both hydrogen or identically selected        (C1-C3)alkyl; R³ and R⁴ are both hydrogen or identically        selected (C1-C3)alkyl;    -   R⁵ and R⁶ are independently selected from the group consisting        of hydrogen, halogen, hydroxyl, (C1-C10)alkyl, cycloalkyl, aryl,        aralkyl, heteroaralkyl, alkoxyl, acyl, acyloxy, aryloxy, amino,        and trialkylsilyloxy;    -   R⁷ is selected from the group consisting of hydrogen and        (C1-C3)alkyl;    -   m is 0, 1, or 2;    -   n is 0, 1, or 2; and    -   p is 0, 1, or 2.

In an alternative embodiment, all else being the same, R¹ and R², and/orR³ and R⁴, are independently selected from the group consisting ofhydrogen and (C1-C3)alkyl.

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is selected from the group consisting of

In one embodiment, R* is selected from the group consisting of

In one embodiment, R* is selected from the group consisting of

In one embodiment, R²¹ and R²², taken together, form a 5-10-memberedcycloalkyl or aromatic ring, or form a 5-10-membered heterocyclic orheteroaromatic ring comprising 1-3 heteroatoms independently selectedfrom the group consisting of N, O, and S.

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In accordance with any one of the foregoing embodiments, in oneembodiment, R⁵ and R⁶ are independently selected from the groupconsisting of hydrogen and (C1-C3)alkyl.

In accordance with any one of the foregoing embodiments, in oneembodiment, m is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, m is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,m is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, n is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, n is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,n is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, p is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, p is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,p is 2.

In accordance with any one of the foregoing embodiments not otherwiseexcluded, in one embodiment, R¹⁰ is

n is 0, p is 0, each instance of R¹² is hydrogen, and R^(H) is selectedfrom the group consisting of aryl and methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

n is O, X′ is CH₂, and R¹¹ is methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

In accordance with any one of the foregoing embodiments, in oneembodiment, R* is a chiral group

of at least 95% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment, R* is a chiral group

of at least 98% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment, R* is a chiral group

of at least 99% enantiomeric excess.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chiral, non-racemic PIDA boronate isrepresented by

wherein:

B is a boron atom having sp³ hybridization;

the carbon atom marked “*” is a chiral carbon atom of at least 90%enantiomeric excess;

-   -   R¹⁰ is selected from the group consisting of

-   -   R¹¹ and each instance of R¹² are independently selected from the        group consisting of hydrogen, halogen, hydroxyl, (C1-C10)alkyl,        cycloalkyl, aryl, aralkyl, heteroaralkyl, alkoxyl, acyl,        acyloxy, aryloxy, amino, and trialkylsilyloxy; or R¹¹ and any        one instance of R¹², or any two instances of R¹², taken        together, form a 3-10-membered ring;    -   X is halogen;    -   each instance of Z is independently selected from the group        consisting of CH and N, provided that no more than two instances        of Z are N;    -   X′ is selected from the group consisting of CR⁵R⁶, O, S, and        NR⁷;    -   R¹ and R² are both hydrogen or identically selected        (C1-C3)alkyl;    -   R⁵ and R⁶ are independently selected from the group consisting        of hydrogen, halogen, hydroxyl, (C1-C10)alkyl, cycloalkyl, aryl,        aralkyl, heteroaralkyl, alkoxyl, acyl, acyloxy, aryloxy, amino,        and trialkylsilyloxy;    -   R⁷ and R³⁰ are independently selected from the group consisting        of hydrogen and (C1-C3)alkyl;    -   n is 0, 1, or 2;    -   p is 0, 1, or 2; and    -   q is 1 or 2.

In an alternative embodiment, all else being the same, R¹ and R² areindependently selected from the group consisting of hydrogen and(C1-C3)alkyl.

In one embodiment, the compound of formula (II) is

In accordance with any one of the foregoing embodiments, in oneembodiment, n is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, n is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,n is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, p is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, p is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,p is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, q is 1. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, q is 2.

In accordance with any one of the foregoing embodiments not otherwiseexcluded, in one embodiment, R¹⁰ is

n is 0, p is 0, each instance of R¹² is hydrogen, and R¹¹ is selectedfrom the group consisting of aryl and methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

n is O, X′ is CH₂, and R¹¹ is methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

In accordance with any one of the foregoing embodiments, in oneembodiment the carbon atom marked “*” is a chiral carbon atom of atleast 95% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment the carbon atom marked “*” is achiral carbon atom of at least 98% enantiomeric excess. In accordancewith any one of the foregoing embodiments, in one embodiment the carbonatom marked “*” is a chiral carbon atom of at least 99% enantiomericexcess.

Customized Hybrid Purification Vessels. In certain embodiments, thepresent invention relates to any one of the aforementioned methods,wherein a customized hybrid purification vessel which contains both a“precipitation chamber” and a “catch-and-release chamber” arranged inseries is used. In this system, a crude cross-coupling reaction istransferred to a first (e.g., upper) chamber filled with hexanes,resulting in rapid and quantitative precipitation of the PIDAboronate-containing product while the residual boronic acid (and mostbyproducts), palladium, and phosphine ligand all remain soluble. Aspreviously noted, simple filtration of this suspension, followed bywashing with Et₂O:MeOH, places the resulting semi-purified, solidchiral, non-racemic PIDA boronate on top of a silica gel plug thatresides in a second (e.g., lower) chamber. This lower chamber is thensubjected to washing with copious volumes of, for example, Et₂O:MeOH98.5:1.5 (v/v) followed by a defined small volume of THF to effect thecatch-and-release silica gel purification. The resulting THF solution ofpurified chiral, non-racemic PIDA boronate is conveniently ready forutilization in subsequent cycles of deprotection and coupling.

Purification/Deprotection of Pida-Protected Organoboronic Acids

The challenges associated with purifying boronic acids include the factthat “the polar and often amphiphilic character tends to make theirisolation and purification difficult” (Hall, D. G. Boronic Acids;Wiley-VCH: Weinheim, Germany, 2005; pp 57-58). Further, “[t]he widelyknown and used boronic acids show variable stability (vinyl-, alkyl-,and alkynylboronic acid are not very stable), and their purification isnot straightforward. Moreover, isolated boronic acids generally containlarge quantities of anhydrides or boroxines, which result in problemsfor determining their stoichiometry” (Darses, S.; Genet, J-P. Chem. Rev.2008, 108, 288-325).

A number of approaches for purifying boronic acids have been developed,but all are limited in their generality. The most basic approach is torecrystallize the boronic acid, typically from an aqueous solution.However, this approach is only efficient if the sample is alreadyrelatively pure and when the temperature-dependent solubility of theboronic acid in water is favorable. When non-polar recrystallizationsolvents are employed, significant dehydration of the boronic acid toafford the boroxine can occur. (Santucci, L.; Gilman, H. J. Am. Chem.Soc. 1958, 80, 193-196). Another approach is “phase switching”liquid/liquid partitioning (Mothana, S.; Grassot, J-M.; Hall, D. G.Angew. Chem. Int. Ed. 2010, 49, 2883-2887). In this approach the boronicacid is converted into the anionic borate species in strong base (pH10), non-anionic organics are washed away, and then the solution isacidified (pH 1-5) to regenerate the boronic acid. This method is notcompatible with boronic acids containing acidic functional groups, basicfunctional groups, or any functionality that is acid- or base-sensitive,including the boronic acid functionality. A solid supported scavengerfor boronic acids based on diethanolamine, abbreviated DEAM-PS, has alsobeen reported (Hall, D. G.; Tailor, J.; Gravel, M. Angew. Chem. Int. Ed.1999, 38, 3064-3067). However, this method is expensive and does notrepresent a practical or scalable solution.

Boronic acids can be purified in a two-step process with theintermediacy of a boronic acid surrogate. For example, boronic acids canbe converted to the corresponding trifluoroborate salt which can becrystallized (Darses, S.; Genet, J-P. Chem. Rev. 2008, 108, 288-325).However, limitations of this approach include the fact that thecrystallization conditions are substrate-specific, large amounts offluoride are used, some impurities co-crystallize with the product, andregenerating the boronic acid from the trifluoroborate is not efficient(Molander, G. A.; Cavalcanti, L. N.; Canturk, B.; Pan, P-S.; Kennedy, L.E. J. Org. Chem. 2009, 74, 7364-7369). Alternatively, boronic acids canbe dehydrated in the presence of a diol (most often pinacol) to form thecorresponding boronic ester. Some aryl boronic esters have morefavorable chromatography, extraction, and crystallization propertiesthan the corresponding boronic acids. However other classes of boronicesters (heteroaryl, alkenyl, alkyl, alkynyl, etc.) tend to have highlyvariable features. Further, as the boronic ester becomes stable enoughto improve its purification properties, the conditions required toregenerate the boronic acid become harsher. For example, converting apinacol boronic ester to the corresponding boronic acid typicallyrequires aqueous acid and an oxidant (often NaIO₄), which limits thegenerality of this approach (Murphy, J. M.; Tzschuck, C. C.; Hartwig, J.F. Org. Lett. 2007, 9, 757-760).

Finally, unstable boronic acids present a particularly challengingproblem. None of the above-mentioned approaches can be used to purifyunstable boronic acids, such as vinyl boronic acids. Remarkably, vinylboronic acid can be generated from vinyl chiral, non-racemic PIDAboronate in greater than 95% purity (Knapp, D. M.; Gillis, E. P.; Burke,M. D. J. Am. Chem. Soc. 2009, 131, 6961-6963).

To address some of the problems noted above, disclosed herein is a“catch and selective release” type method developed for chiral,non-racemic PIDA boronate hydrolysis. Specifically, a THF solution of achiral, non-racemic PIDA boronate (reactivity=OFF) is mixed withsolid-supported ammonium hydroxide reagent (such as Amberlyst A26(OH);see T. M. Morwick, J. Comb. Chem. 2006, 8, 649-651) to promote the PIDAhydrolysis. At this point, both the cleaved PIDA ligand (likely in theform of PIDA²⁻Na+₂) and the boronic acid (likely in the form of thecorresponding anionic boron-′ate′ complex; see D. G. Hall, J. Tailor, M.Gravel, Angew. Chem. Int. Ed. 1999, 38, 3064-3067) remain trapped in theresin (the “catch”). It was determined that subsequent treatment with aTHF solution of AcOH (see M. G. Siegel, P. J. Hahn, B. A. Dressman, J.E. Fritz, J. R. Grunwell, S. W. Kaldor, Tetrahedron Lett. 1997, 38,3357-3360) results in “selective release” of only the boronic acid(reactivity=ON), while the cleaved PIDA ligand conveniently remainstrapped in the resin under these mildly acidic conditions. Transferringthis THF/AcOH/boronic acid solution to a new vial containing K₂CO₃, 4 Åmolecular sieves, and Celite®, followed by bubbling argon through themixture and filtration yields a neutralized, mostly anhydrous, anddeoxygenated solution of freshly-prepared boronic acid in THF, ready forthe next cross-coupling reaction.

One aspect of the invention relates to the deprotection of a PIDAboronate, comprising the step of contacting a solution comprising thechiral, non-racemic PIDA boronate and a solvent with a solid-supportedammonium hydroxide reagent, thereby deprotecting the chiral, non-racemicPIDA boronate and forming a boronic acid and a free PIDA ligand.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the solvent comprises THF.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the solid-supported ammonium hydroxidereagent binds the PIDA.

In certain embodiments, the present invention relates to any one of theaforementioned methods, further comprising the steps of removing thesolvent by filtration, thereby leaving the boronic acid and PIDA ligandtrapped inside the solid-supported ammonium hydroxide reagent; andadding additional solvent.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the additional solvent is THF.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the solid-supported ammonium hydroxidereagent is washed with an organic solution comprising an organic solventand a mild or strong acid in a quantity greater than that needed toneutralize the solid-supported ammonium hydroxide reagent, therebyeluting the boronic acid.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the solid-supported ammonium hydroxidereagent is washed with a THF solution comprising a mild or strong acid,thereby eluting the boronic acid.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the solid-supported ammonium hydroxidereagent is washed with a THF solution comprising acetic acid, therebyeluting the boronic acid.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the eluted boronic acid is treated withbase to neutralize the acid (e.g., acetic acid).

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the base is potassium carbonate.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the solid-supported ammonium hydroxidereagent is washed with a 1,4-dioxane solution comprising hydrochloricacid, thereby eluting the boronic acid.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the solid-supported ammonium hydroxidereagent is a strong base anion exchange resin, e.g., Amberlite IRA-400(OH⁻ form), Amberlite IRA 420 (OH⁻ form), Amberlite IRA 410 (OH⁻ form),Amberlite IRN-150, Amberlite IRA 900 (OH⁻ form), Amberlite IRA 904 (OH⁻form), Amberlite IRA 910 (OH⁻ form), Amberlite A5836, Amberlyst A26 (OH⁻form), Ambersep 900, Dowex-1 (OH⁻ form), Dowex-3 (OH⁻ form), Dowex 1-X4(OH⁻ form), Dowex 1-I 9880, Dowex 1-10131, Dowex 550 A (OH⁻ form), orAmberjet 4400.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the solid-supported ammonium hydroxidereagent is a strong base, type 1, anionic, macroreticular polymericresin based on crosslinked styrene divinylbenzene copolymer containingquaternary ammonium groups, e.g., Amberlyst A26 (OH⁻ form) (Rohm andHaas, Philadelphia, Pa.).

An aspect of the invention relates to a method of deprotecting a PIDAboronate, comprising the step of contacting a solution comprising thechiral, non-racemic PIDA boronate and a solvent with an aqueous solutionof NaOH, thereby deprotecting the chiral, non-racemic PIDA boronate andforming a boronic acid and free PIDA ligand. This method is particularlyuseful in connection with acid-sensitive substrates (boronic acids)because it does not include exposure to acid for elution from a solidsupport.

Because water will be removed in subsequent steps, it is generallydesirable to limit the volume of the aqueous component (solution ofNaOH) introduced into the system to a relatively small amount, e.g.,about 25-33 percent of the volume of the solution comprising the chiral,non-racemic PIDA boronate and its solvent.

In certain embodiments, the present invention relates to theaforementioned method, wherein the solvent comprises THF.

In certain embodiments, the present invention relates to theaforementioned method, wherein the solvent is THF. In one embodiment,the THF is dry and deoxygenated.

In certain embodiments, the present invention relates to theaforementioned method, further comprising the steps of adding diethylether, thereby generating a biphasic mixture comprising an organic phasecomprising the boronic acid and free PIDA ligand, and an aqueous phase;and separating the organic phase comprising the boronic acid and freePIDA ligand from the aqueous phase. The step of adding diethyl ether canoptionally include adding a reagent effective for quenching thereaction. In one embodiment, the reagent effective for quenching thereaction is a phosphate buffer. Again, because water will be removed insubsequent steps, it is generally desirable to limit the total amount ofwater introduced into the system to a relatively small amount, e.g.,about 25-33 percent of the volume of the combined solution comprisingthe PIDA boronate, its organic solvent, and the aqueous solution ofNaOH. In one embodiment, the phosphate buffer is added in an amountapproximately equal to the volume of the aqueous solution of NaOH.

In certain embodiments, the present invention relates to any one of theaforementioned methods, further comprising the step of contacting theorganic phase with one or more drying agents selected from the groupconsisting of magnesium sulfate, diatomaceous earth, and molecularsieves, thereby drying the organic phase comprising the boronic acid andfree PIDA ligand. A diatomaceous earth can be, for example, Celite®(Fluka/Sigma-Aldrich, St. Louis, Mo.; Celite Corp., Lompoc, Calif.).

In certain embodiments, the present invention relates to any one of theaforementioned methods, further comprising the step of deoxygenating thedried organic phase comprising the boronic acid and free PIDA ligand. Inone embodiment, the deoxygenation is accomplished by bubbling dryoxygen-free gas through the organic phase comprising the boronic acidand free PIDA ligand. In one embodiment, the oxygen-free gas is argon.

Automated Small Molecule Synthesizers

With robust and general methods for the purification and deprotection ofPIDA boronates in hand, an apparatus with the capacity forfully-automated synthesis of small molecules via ICC (FIG. 4) wasdesigned and built. In certain embodiments, this apparatus is comprisedof three modules, each designed to promote a deprotection (D),cross-coupling (CC), or purification (P) step required to execute theICC scheme described herein. In certain embodiments, all materials aretransferred between modules as solutions manipulated by a series of mainsyringe pumps (e.g., eight) coordinated with a suite of switchablevalves (J-KEM Scientific). In certain embodiments, all of the syringepumps are driven by a computer running a custom-made software program.One embodiment of the machine is depicted in FIG. 4; additional detailsregarding this machine are provided in the Exemplification below.

Reaction System Design. In certain embodiments, the cross-couplingreactions are run in polypropylene tubes purchased from Luknova, item#FC003012. The dimensions of the tube are 21 mm×120 mm (ID×length). Thebottom of the tube is fitted with a 21 mm diameter×4 mm tall frit. Ontop of this frit is secured via metal wire a 13 mm diameter×4 mm tallfrit. On top of the frit is placed a large stir bar containing arare-earth magnet (Big Science Inc., SBM-1508-REH). The bottom of thetube is accessed through a male Luer tip, while the top of the tube issealed with an air-tight, threaded cap containing a female Luer port.The tube holds a solvent volume of up to 25 mL. The tubes are placed inan aluminum heating block that was custom fabricated. The heating blockholds up to nine reaction tubes. The tubes are held 3 cm above thesurface of the stir plate, where the bottom 4 cm of the tube is jacketedby the heating block. The tubing to access the bottom of the reactiontube goes through a hole in the side of the block near the bottom.

The use of a polypropylene tube appears to be important in simplifyingthe engineering of the reaction tube. Specifically, the material is agood insulator such that only the portion that is jacketed by theheating block becomes hot. When the heating block is heated to 60° C.,the reaction solution reaches 60° C. within several minutes. However,the portion of the tube that is not jacketed remains at roomtemperature, acting as a condenser, and thus the vapor above the solventremains at room temperature. When other materials such as glass wereused, the portion of the tube above the heating block became hot and thesolution quickly evaporated. Thus, if glass were to be used instead ofpolypropylene, there would need to be an additional cooling element inorder to keep the solution from escaping.

In certain embodiments of the system the tubes in the reaction block arestirred constantly, regardless of whether there is solution inside thetube. This keeps the system simple since the stir plate does not need tobe turned on or off, and further, the start and stop times of thereactions within the block do not need to be coordinated. However,during prolonged stirring the stir bar in the tube acts as a mortar andthe frit as a pestle, such that the base becomes finely ground into thepores of the frit. Further, the stir bar may be damaging the top of thefrit even in the absence of base. In these situations it becomes nearlyimpossible to withdraw solutions through the frit since the top surfaceof the frit is clogged and/or damaged. To overcome this limitation areaction tube was designed to contain two frits of different sizes (FIG.8). This way the stir bar only contacts the smaller top frit, and evenif the top surface of this frit is damaged or clogged, the solution canbe withdrawn through the sides of the small frit or through the spacesopen only to the larger frit. The wire is necessary to secure the topfrit so that it does not rotate sideways during the reaction to becomeperpendicular to the larger frit. In certain embodiments, a single fritcould be fabricated to have a shape similar to the combined frits.

Purification System Design. The chromatographic properties of PIDAboronates that enable the simple purification approach are discussedabove. Below is described how the engineering of the system supports thecatch-and-release chromatography and precipitation-based purification.

Because diluting the crude THF reaction solution with hexanes will causeimmediate precipitation of the chiral, non-racemic PIDA boronateproduct, the mixing of THF and hexanes must occur in a container ofsufficient volume to hold the precipitated product. The solvents mustalso be thoroughly mixed so that the solution is homogeneous. Finally,the addition of hexanes to the THF solution also causes reactionbyproducts to become insoluble. In some cases these byproducts aresticky or form a very fine precipitate that can clog a frit. In certainembodiments, a custom designed precipitation chamber in which to mix thecrude THF solution and hexanes can be used (FIG. 9). In certainembodiments, the precipitation chamber contains Celite® which scavengesthe sticky impurities that precipitate and keeps this materialdistributed throughout the Celite® so it does not clog the frit. Incertain embodiments, a stir bar in the chamber ensures proper mixing.However, it was observed that if the stir bar stirs continuously forseveral hours, the Celite® in the tube becomes so finely ground that itcan pass through the frit and clog downstream processes. To solve thisproblem, after the precipitation chamber is filled with solvent andmixed, the solvent is withdrawn so that the stir bar becomes imbedded inthe dry Celite® and does not stir. In other words, the stir bar can bemade to stir only when it is needed—i.e., when there is solvent in theprecipitation chamber—and, therefore, this process does not requireturning the stir plate on/off or coordinating the stirring of otherprocesses that use the same stir plate. In certain embodiments,3-aminopropyl-functionalized silica gel is placed in the precipitationchamber to scavenge palladium from a crude reaction solution.

In certain embodiments, the precipitation chamber is first filled withhexanes via the auxiliary pump (thus wetting the SiO₂ column withhexanes in the process). Then, a THF reaction solution is added from thetop. The main pump does not handle both the hexanes and the THF solutionbecause residual hexanes in the syringe might cause the chiral,non-racemic PIDA boronate product to precipitate in the syringe.Further, the main pump does not withdraw the waste THF:hexanes solutionfor this reason and to reduce contamination. Thus, once the solvents aremixed in the precipitation chamber, the solution is withdrawn by theauxiliary pump through the SiO₂ column and then sent to waste. Next,Et₂O with MeOH is added to the precipitation chamber, mixed, and thenwithdrawn through the SiO₂ column and sent to waste. This process isrepeated with Et₂O. At this point the pure chiral, non-racemic PIDAboronate product remains as a precipitate in the precipitation chamberor is at the very top of the SiO₂ column. The auxiliary pump theninjects THF through the bottom of the SiO₂ column, out through the topand through to the precipitation chamber. Thus, it does not matter ifthe chiral, non-racemic PIDA boronate product is initially in the SiO₂column or in the precipitation chamber, since it will be dissolved inTHF at either location. This system reduces the amount of THF used toelute/dissolve the product, allowing the solution to be used in the nextreaction without further concentration. After the THF has been mixed inthe precipitation chamber for about 30 minutes, it is withdrawn by themain pump through the 3-way union without again passing through the SiO₂column.

Some important features of this setup are: the precipitation eventoccurs in a mixing chamber; the mixing chamber contains scavengers(Celite® and functionalized silica gel); the stirring can be controlledin a simple way; the precipitation chamber and SiO₂ column are spatiallyseparated; and the configuration of pumps allows solvents to be addedand withdrawn at various junctions throughout the process.

Software. The software that controls the machine can be described ashaving three levels of complexity: the basic level, the functionallevel, and the developed level. The basic level represents essentiallythe combination of 1's and 0's that can be sent to the equipment to movethe syringe pumps and valves. The functional level represents thesimplest commands to move the equipment that could be understood by aperson looking at the computer code. The developed level representssoftware specifically tailored to the automated synthesis machine thatcan be used by non-experts to modify how the synthesis is performed. Thebasic level is inherent to the equipment manufactured by Kloehn. Thefunctional level came from source code provided by J-KEM when theequipment was purchased. The functional level is source code written inVB.NET that packages the commands of the basic level into easilyexecuted subroutines. The developed level was custom designed andwritten in VB.NET based on the source code provided in the functionallevel.

More specifically, the machine is composed of a number of syringe pumpsand valves that are OEM parts from Kloehn. The syringe pumps and valveswere repackaged and sold by J-KEM as a custom piece of hardware. Theequipment is controlled via a RS-485 serial port that sends and receivessimple text string commands written in machine language specific to theKloehn parts. Thus, on the simplest level the machine can be controlledby sending simple text strings such as “/xR”, but these commands areunintelligible to anyone using the equipment. The equipment shipped fromJ-KEM came with source code written in VB.NET that provides subroutinesto move the syringe pump to specific positions, change valves tospecific positions, control the rate at which the syringe moves, andopen/close solenoid valves. The code that was developed uses thesubroutines from the code provided by J-KEM. The source code from J-KEMcould be removed and the software could communicate with the equipmentdirectly without losing functionality. However, the source code fromJ-KEM would not be by itself enough to run an automated synthesis. Thus,it was necessary to create software to enable the development of theautomated synthesis machine. Details regarding certain embodiments ofthe software can be found in the Exemplification.

Automated Synthesizers. One aspect of the invention relates to anautomated small molecule synthesizer comprising: (a) a deprotectionmodule, in fluid communication with (b) a drying and degassing module,in fluid communication with (c) a reaction module, in fluidcommunication with (d) a purification module; at least one pump whichcan move liquid from one module to another; and a computer equipped withsoftware; wherein all of the modules are under the control of thecomputer.

In one embodiment, the deprotection module comprises immobilized orsolid-supported base, e.g., NaOH, as described herein. In oneembodiment, the deprotection module is constructed and arranged so as toperform deprotection with aqueous base, e.g., aqueous NaOH, as describedherein.

In one embodiment, the purification module comprises a combined (or“hybrid”) precipitation and catch-and-release module.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thedeprotection module comprises a deprotection chamber which comprises afirst opening at the top of the chamber, a second opening at the bottomof the chamber, a first frit covering the second opening, and asolid-supported ammonium hydroxide reagent.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thedeprotection chamber comprises a cylindrical tube.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the deprotection chamber is a polypropylenecylindrical tube.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the deprotection chamber has a length of betweenabout 100 mm and 140 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the deprotection chamber has a length of about 120mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the deprotection chamber has an interior diameter ofbetween about 18 mm and about 24 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the deprotection chamber has an interior diameter ofabout 21 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the deprotection chamber has a volume of about 25mL.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thesolid-supported ammonium hydroxide reagent is a strong base anionexchange resin, e.g., Amberlite IRA-400 (OH⁻ form), Amberlite IRA 420(OH⁻ form), Amberlite IRA 410 (OH⁻ form), Amberlite IRN-150, AmberliteIRA 900 (OH⁻ form), Amberlite IRA 904 (OH⁻ form), Amberlite IRA 910 (OH⁻form), Amberlite A5836, Amberlyst A26 (OH⁻ form), Ambersep 900, Dowex-1(OH⁻ form), Dowex-3 (OH⁻ form), Dowex 1-X4 (OH⁻ form), Dowex 1-I 9880,Dowex 1-10131, Dowex 550 A (OH⁻ form), or Amberjet 4400.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thesolid-supported ammonium hydroxide reagent is a strong base, type 1,anionic, macroreticular polymeric resin based on crosslinked styrenedivinylbenzene copolymer containing quaternary ammonium groups, e.g.,Amberlyst A26 (OH⁻ form).

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thedeprotection module further comprises a source of gas; wherein thesource of gas can be placed in fluid communication with the deprotectingchamber.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the dryingand degassing module comprises a combined drying and degassing chamberwhich comprises a first opening at the top of the combined drying anddegassing chamber, a second opening at the bottom of the combined dryingand degassing chamber, a first frit covering the second opening, and aplunger; and the drying and degassing module is in fluid communicationwith the deprotection module.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecombined drying and degassing chamber further comprises a diatomaceousearth, e.g., Celite®.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecombined drying and degassing chamber further comprises activatedmolecular sieves.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein themolecular sieves are 4 angstrom, 8-12 mesh.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecombined drying and degassing chamber further comprises potassiumcarbonate.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the fluidcommunication is a result of the connection of the second opening of thedeprotection chamber to the second opening of the combined drying anddegassing chamber.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecombined drying and degassing chamber comprises a cylindrical tube.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the combined drying and degassing chamber is apolypropylene cylindrical tube.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the combined drying and degassing chamber has alength of between about 100 mm and 140 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the combined drying and degassing chamber has alength of about 120 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the combined drying and degassing chamber has aninterior diameter of between about 18 mm and about 24 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the combined drying and degassing chamber has aninterior diameter of about 21 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the combined drying and degassing chamber has avolume of about 25 mL.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, further comprisinga source of argon.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the argoncan be placed in fluid communication with the combined drying anddegassing chamber to sparge the contents of the combined drying anddegassing chamber; and the plunger prevents solids from lifting duringsparging.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the firstopening of the combined drying and degassing chamber is vented to aninert gas atmosphere which is maintained near atmospheric pressure viaventing through an oil-filled bubbler.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the argoncan be placed in fluid communication with the combined drying anddegassing chamber through the second opening of the tube of the combineddrying and degassing chamber while the first opening of the tube of thecombined drying and degassing chamber is vented to an inert gasatmosphere.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the dryingand degassing module comprises a drying chamber and a degassing chamber;the drying chamber comprises a first opening at the top of the dryingchamber, a second opening at the bottom of the drying chamber, a firstfrit covering the second opening, and a plunger; the degassing chambercomprises a first opening at the top of the degassing chamber and asecond opening at the bottom of the degassing chamber; the dryingchamber is in fluid communication with the degassing chamber; and thedegassing chamber is in fluid communication with the deprotectionmodule.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the dryingchamber further comprises a diatomaceous earth, such as Celite®.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the dryingchamber further comprises activated molecular sieves.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein themolecular sieves are 4 angstrom, 8-12 mesh.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the dryingchamber further comprises potassium carbonate.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the fluidcommunication between the drying chamber and the degassing chamber is aresult of the connection of the second opening of the drying chamber tothe second opening of the degassing chamber.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the fluidcommunication between the drying and degassing module and the degassingchamber is a result of the connection of the second opening of thedegassing chamber to the deprotection module.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the dryingchamber comprises a cylindrical tube.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the drying chamber is a polypropylene cylindricaltube.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the drying chamber has a length of between about 100mm and 140 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the drying chamber has a length of about 120 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the drying chamber has an interior diameter ofbetween about 18 mm and about 24 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the drying chamber has an interior diameter of about21 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the drying chamber has a volume of about 25 mL.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thedegassing chamber comprises a cylindrical tube.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the degassing chamber is a polypropylene cylindricaltube.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the degassing chamber has a length of between about100 mm and 140 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the degassing chamber has a length of about 120 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the degassing chamber has an interior diameter ofbetween about 18 mm and about 24 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the degassing chamber has an interior diameter ofabout 21 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the degassing chamber has a volume of about 25 mL.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, further comprisinga source of argon.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the argoncan be placed in fluid communication with the degassing chamber tosparge the contents of the degassing chamber.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the firstopening of the degassing chamber is vented to an inert gas atmospherewhich is maintained near atmospheric pressure via venting through anoil-filled bubbler.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the argoncan be placed in fluid communication with the degassing chamber throughthe second opening of the tube of the degassing chamber while the firstopening of the tube of the degassing chamber is vented to an inert gasatmosphere.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thereaction module comprises a reaction chamber which comprises a firstopening at the top of the reaction chamber, a second opening at thebottom of the reaction chamber, a first frit covering the secondopening, and a stir bar; wherein the reaction module is in fluidcommunication with the drying and degassing module.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thereaction module comprises a third opening at the top of the reactionchamber through which a liquid can be added to the reaction chamberwithout contacting the sidewalls or the bottom of the reaction chamber.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the firstopening of reaction chamber is vented to an inert atmosphere.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the firstopening of the reaction chamber is fitted with a fritted tube to preventfine solids from escaping from the reaction chamber.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the firstopening of the reaction chamber is vented to an inert atmospheremaintained near atmospheric pressure via venting through an oil-filledbubbler.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein both thesecond opening and third opening of the reaction chamber are in fluidcommunication with the second opening of the drying and degassingchamber at the same time.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thereaction chamber comprises a cylindrical tube.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the reaction chamber is a polypropylene cylindricaltube.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the reaction chamber has a length of between about100 mm and 140 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the reaction chamber has a length of about 120 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the reaction chamber has an interior diameter ofbetween about 18 mm and about 24 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the reaction chamber has an interior diameter ofabout 21 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the reaction chamber has a volume of about 25 mL.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thereaction chamber further comprises a second frit between the stir barand the first frit; wherein the second frit is smaller than the firstfrit.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the secondfrit and the first frit are held together with a wire, to prevent thesecond frit from turning perpendicular to the first frit.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the firstfrit is disc-shaped; the first frit has a diameter of between about 18mm and about 24 mm; and the first frit has a height between about 2 mmand about 6 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the firstfrit is disc-shaped; the first frit has a diameter of about 21 mm; andthe first frit has a height of about 4 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the secondfrit is disc-shaped; the second frit has a diameter between about 16 mmand about 10 mm; and the second frit has a height between about 2 mm andabout 6 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the secondfrit is disc-shaped; the second frit has a diameter of about 13 mm; andthe second frit has a height of about 4 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the shapeof the first frit is that of a first disc on top of a second disc;wherein the diameter of the first disc is smaller than the diameter ofthe second disc.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the shapeof the first frit prevents solids from passing through the secondopening of the reaction chamber.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thereaction module further comprises a stir plate which turns the stir bar.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thereaction module further comprises a heating block which can heat thecontents of the reaction chamber.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein at least aportion of the reaction chamber is jacketed by the heating block.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thereaction chamber further comprises a transition metal salt.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thetransition metal salt is adsorbed onto a solid.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thetransition metal salt is palladium acetate.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the solidonto which the transition metal salt is adsorbed is cesium carbonate.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thereaction chamber further comprises a phosphine ligand.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thephosphine ligand is adsorbed onto a solid.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thephosphine ligand is S-Phos(2-dicyclohexylphosphino-2′,6′-dimethoxybiphenyl).

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecatalyst is derived from an air-stable palladium precatalyst.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the solidonto which the phosphine ligand is adsorbed is cesium carbonate.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thereaction chamber further comprises a base.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the basein the reaction chamber is potassium hydroxide.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thereaction run in the reaction chamber is a cross-coupling reaction.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thereaction run in the reaction chamber is selected from the groupconsisting of a Suzuki-Miyaura coupling, an oxidation, a Swernoxidation, a “Jones reagents” oxidation, a reduction, an Evans' aldolreaction, an HWE olefination, a Takai olefination, an alcoholsilylation, a desilylation, a p-methoxybenzylation, an iodination, aNegishi cross-coupling, a Heck coupling, a Miyaura borylation, a Stillecoupling, and a Sonogashira coupling.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chemical reaction is selected fromepoxidation, nucleophilic substitution, electrophilic substitution,oxidation, dihydroxylation, carbonylation, alkenation, cyclopropanation,cycloaddition, conjugate addition, Michael addition, Diels-Alderreaction, and transition metal-catalyzed cross-coupling reaction.

In accordance with any one of the foregoing embodiments, in oneembodiment, the transition metal-catalyzed cross-coupling reaction is aSuzuki-Miyaura reaction.

In accordance with any one of the foregoing embodiments, in oneembodiment, the chemical reaction is epoxidation.

In accordance with any one of the foregoing embodiments, in oneembodiment, the epoxidation is selected from the group consisting ofSharpless epoxidation and Jacobsen epoxidation.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thereaction run in the reaction chamber is a Suzuki-Miyaura coupling.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thechemical reaction run in the reaction chamber comprises the step ofcontacting a chiral, non-racemic PIDA boronate with a reagent, whereinthe chiral, non-racemic PIDA boronate comprises a boron having an sp³hybridization, a PIDA protecting group bonded to the boron, and anorganic group bonded to the boron through a boron-carbon bond; theorganic group is chemically transformed, and the boron is not chemicallytransformed.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thechiral, non-racemic PIDA boronate is represented by

wherein:

B is a boron atom having sp³ hybridization;

-   -   R* is a chiral group

of at least 90% enantiomeric excess;

-   -   R²¹ and R²² are independently selected from the group consisting        of hydrogen, alkyl, cycloalkyl, heterocyclyl, aryl, heteroaryl,        aralkyl, and heteroaralkyl; or R²¹ and R²², taken together, form        a 5-10-membered cycloalkyl or aromatic ring, or form a        5-10-membered heterocyclic or heteroaromatic ring comprising 1-3        heteroatoms independently selected from the group consisting of        N, O, and S;    -   R²³ is selected from the group consisting of hydrogen, alkyl,        cycloalkyl, heterocyclyl, aryl, heteroaryl, aralkyl, and        heteroaralkyl;    -   R¹⁰ is selected from the group consisting of

-   -   R¹¹ and each instance of R¹² are independently selected from the        group consisting of hydrogen, halogen, hydroxyl, (C1-C10)alkyl,        cycloalkyl, aryl, aralkyl, heteroaralkyl, alkoxyl, acyl,        acyloxy, aryloxy, amino, and trialkylsilyloxy; or R¹¹ and any        one instance of R¹², or any two instances of R¹², taken        together, form a 3-10-membered ring;    -   X is halogen;    -   each instance of Z is independently selected from the group        consisting of CH and N, provided that no more than two instances        of Z are N;    -   X′ is selected from the group consisting of CR⁵R⁶, O, S, and        NR⁷;    -   R¹ and R² are both hydrogen or identically selected        (C1-C3)alkyl;    -   R³ and R⁴ are both hydrogen or identically selected        (C1-C3)alkyl;    -   R⁵ and R⁶ are independently selected from the group consisting        of hydrogen, halogen, hydroxyl, (C1-C10)alkyl, cycloalkyl, aryl,        aralkyl, heteroaralkyl, alkoxyl, acyl, acyloxy, aryloxy, amino,        and trialkylsilyloxy;    -   R⁷ is selected from the group consisting of hydrogen and        (C1-C3)alkyl;    -   m is 0, 1, or 2;    -   n is 0, 1, or 2; and    -   p is 0, 1, or 2.

In an alternative embodiment, all else being the same, R¹ and R², and/orR³ and R⁴, are independently selected from the group consisting ofhydrogen and (C1-C3)alkyl.

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is selected from the group consisting of

In one embodiment, R* is selected from the group consisting of

In one embodiment, R* is selected from the group consisting of

In one embodiment, R²¹ and R²², taken together, form a 5-10-memberedcycloalkyl or aromatic ring, or form a 5-10-membered heterocyclic orheteroaromatic ring comprising 1-3 heteroatoms independently selectedfrom the group consisting of N, O, and S.

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In one embodiment, R* is

In accordance with any one of the foregoing embodiments, in oneembodiment, R⁵ and R⁶ are independently selected from the groupconsisting of hydrogen and (C1-C3)alkyl.

In accordance with any one of the foregoing embodiments, in oneembodiment, m is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, m is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,m is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, n is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, n is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,n is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, p is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, p is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,p is 2.

In accordance with any one of the foregoing embodiments not otherwiseexcluded, in one embodiment, R¹⁰ is

n is 0, p is 0, each instance of R¹² is hydrogen, and R″ is selectedfrom the group consisting of aryl and methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

n is O, X′ is CH₂, and R¹¹ is methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

In accordance with any one of the foregoing embodiments, in oneembodiment, R* is a chiral group

of at least 95% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment, R* is a chiral group

of at least 98% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment, R* is a chiral group

of at least 99% enantiomeric excess.

In certain embodiments, the present invention relates to any one of theaforementioned methods, wherein the chiral, non-racemic PIDA boronate isrepresented by

wherein:

B is a boron atom having sp³ hybridization;

the carbon atom marked “*” is a chiral carbon atom of at least 90%enantiomeric excess;

-   -   R¹⁰ is selected from the group consisting of

-   -   R¹¹ and each instance of R¹² are independently selected from the        group consisting of hydrogen, halogen, hydroxyl, (C1-C10)alkyl,        cycloalkyl, aryl, aralkyl, heteroaralkyl, alkoxyl, acyl,        acyloxy, aryloxy, amino, and trialkylsilyloxy; or R¹¹ and any        one instance of R¹², or any two instances of R¹², taken        together, form a 3-10-membered ring;    -   X is halogen;    -   each instance of Z is independently selected from the group        consisting of CH and N, provided that no more than two instances        of Z are N;    -   X′ is selected from the group consisting of CR⁵R⁶, O, S, and        NR⁷;    -   R¹ and R² are both hydrogen or identically selected        (C1-C3)alkyl;    -   R⁵ and R⁶ are independently selected from the group consisting        of hydrogen, halogen, hydroxyl, (C1-C10)alkyl, cycloalkyl, aryl,        aralkyl, heteroaralkyl, alkoxyl, acyl, acyloxy, aryloxy, amino,        and trialkylsilyloxy;    -   R⁷ and R³⁰ are independently selected from the group consisting        of hydrogen and (C1-C3)alkyl;    -   n is 0, 1, or 2;    -   p is 0, 1, or 2; and    -   q is 1 or 2.

In an alternative embodiment, all else being the same, R¹ and R² areindependently selected from the group consisting of hydrogen and(C1-C3)alkyl.

In one embodiment, the compound of formula (II) is

In accordance with any one of the foregoing embodiments, in oneembodiment, n is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, n is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,n is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, p is 0. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, p is 1. Alternatively, inaccordance with any one of the foregoing embodiments, in one embodiment,p is 2.

In accordance with any one of the foregoing embodiments, in oneembodiment, q is 1. Alternatively, in accordance with any one of theforegoing embodiments, in one embodiment, q is 2.

In accordance with any one of the foregoing embodiments not otherwiseexcluded, in one embodiment, R¹⁰ is

n is 0, p is 0, each instance of R¹² is hydrogen, and R¹¹ is selectedfrom the group consisting of aryl and methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

n is O, X′ is CH₂, and R¹¹ is methyl.

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

Alternatively, in accordance with any one of the foregoing embodimentsnot otherwise excluded, in one embodiment, R¹⁰ is

In accordance with any one of the foregoing embodiments, in oneembodiment the carbon atom marked “*” is a chiral carbon atom of atleast 95% enantiomeric excess. In accordance with any one of theforegoing embodiments, in one embodiment the carbon atom marked “*” is achiral carbon atom of at least 98% enantiomeric excess. In accordancewith any one of the foregoing embodiments, in one embodiment the carbonatom marked “*” is a chiral carbon atom of at least 99% enantiomericexcess.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thepurification module comprises a precipitation chamber and a silicacolumn; the precipitation chamber comprises a first opening at the topof the precipitation chamber, a second opening at the bottom of theprecipitation chamber, a first frit covering the second opening, a stirbar, and a diatomaceous earth (such as Celite®); and the silica columncomprises a first opening at the top of the column, a second opening atthe bottom of the column, a second frit covering the top opening of thecolumn, a third frit covering the bottom opening of the column, andsilica; wherein the purification module is in fluid communication withthe reaction module.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein theprecipitation chamber comprises a cylindrical tube.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the precipitation chamber is a polypropylenecylindrical tube.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the precipitation chamber has a length of betweenabout 100 mm and 140 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the precipitation chamber has a length of about 120mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the precipitation chamber has an interior diameterof between about 18 mm and about 24 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the precipitation chamber has an interior diameterof about 21 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the precipitation chamber has a volume of about 25mL.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein theprecipitation chamber further comprises a resin which scavenges metals.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein theprecipitation chamber further comprises activated charcoal.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thepurification module further comprises a stir plate which turns the stirbar.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thediatomaceous earth (e.g., Celite®) in the precipitation chamber preventsthe stir bar from turning if there is no solvent in the precipitationchamber.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the firstfrit of the precipitation chamber keeps the diatomaceous earth in theprecipitation chamber.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the silicacolumn is a cylindrical tube.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the silica column is a polypropylene cylindricaltube.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the silica column has a length of between about 100mm and 140 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the silica column has a length of about 120 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the silica column has an interior diameter ofbetween about 18 mm and about 24 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the silica column has an interior diameter of about21 mm.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thecylindrical tube of the silica column has a volume of about 25 mL.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the secondfrit of the silica column and third frit of the silica column keep thesilica in the silica column.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the silicais functionalized with amino groups.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thepurification module further comprises an auxiliary pump.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, further comprisinga solvent reservoir containing hexane.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thepurification module is in fluid communication with the reservoir ofhexane; and the auxiliary pump provides hexane from the reservoir to theprecipitation chamber by passing the hexane into the silica columnthrough the second opening of the silica column, out of the silicacolumn through the first opening of the silica column, and into theprecipitation chamber through the second opening of the precipitationchamber.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein theauxiliary pump can remove the hexane by passing the hexane into thesecond opening of the precipitation chamber, through the first openingof the silica column and out the second opening of the silica column.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, further comprisinga solvent reservoir containing diethyl ether.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thepurification module is in fluid communication with the reservoir ofdiethyl ether; and the auxiliary pump provides diethyl ether from thereservoir to the precipitation chamber by passing the diethyl ether intothe silica column through the second opening of the silica column, outof the silica column through the first opening of the silica column, andinto the precipitation chamber through the second opening of theprecipitation chamber.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein theauxiliary pump can remove the diethyl ether by passing the diethyl etherinto the second opening of the precipitation chamber, through the firstopening of the silica column and out the second opening of the silicacolumn.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, further comprisinga solvent reservoir containing diethyl ether containing 1.5% methanol byvolume.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thepurification module is in fluid communication with the reservoir ofdiethyl ether containing 1.5% methanol by volume; and the auxiliary pumpprovides diethyl ether containing 1.5% methanol by volume from thereservoir to the precipitation chamber by passing the diethyl ether intothe silica column through the second opening of the silica column, outof the silica column through the first opening of the silica column, andinto the precipitation chamber through the second opening of theprecipitation chamber.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein theauxiliary pump can remove the diethyl ether containing 1.5% methanol byvolume by passing the diethyl ether containing 1.5% methanol by volumeinto the second opening of the precipitation chamber, through the firstopening of the silica column and out the second opening of the silicacolumn.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, further comprisinga waste container; wherein the second opening of the silica column is influid communication with the waste container.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, further comprisinga solvent reservoir containing THF.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein thepurification module is in fluid communication with the reservoir of THF;and the auxiliary pump provides THF from the reservoir to theprecipitation chamber by passing the THF into the silica column throughthe second opening of the silica column, out of the silica columnthrough the first opening of the silica column, and into theprecipitation chamber through the second opening of the precipitationchamber.

In certain embodiments, the present invention relates to any one of theaforementioned automated small molecule synthesizers, wherein the secondopening of the precipitation chamber can be placed in fluidcommunication with the first opening of the silica column via athree-way valve; wherein a first port on the valve is connected to thesecond opening of the precipitation chamber, a second port on the valveis connected to the first opening of the silica column, and a third porton the valve can be used to withdraw a solution from the precipitationchamber without passing the solution through the silica column.

Another aspect of the invention relates to any one of the aforementionedautomated small molecule synthesizers, comprising: one or moredeprotection modules; one or more drying and degassing modules; one ormore reaction modules; one or more purification modules; at least onepump which can move liquid from one module to another; and a computerequipped with software; wherein all of the modules are under the controlof the computer.

Another aspect of the invention relates to any one of the aforementionedautomated small molecule synthesizers comprising: a plurality ofdeprotection modules; a plurality of drying and degassing modules; aplurality of reaction modules; a plurality of purification modules; atleast one pump which can move liquid from one module to another; and acomputer equipped with software; wherein all of the modules are underthe control of the computer.

Alternative Embodiment Using Aqueous Deprotection Module. The aqueousdeprotection module consists of equipment necessary to complete asolution-phase aqueous base-mediated chiral, non-racemic PIDA boronatedeprotection, a separation of the resulting biphasic mixture, apredrying and drying of the organic layer (e.g., ethereal solution ofthe boronic acid), and a deoxygenation/concentration of the driedorganic layer in preparation for a cross-coupling.

Specifically, two syringe pumps and an argon solenoid are utilized inthe new deprotection module (FIG. 9). The primary syringe pump, which isused for the majority of liquid handling during an entire sequence,handles organic solvents and solutions. A dedicated aqueous syringe pumpis utilized to handle all aqueous reagents (water, 0.5 M, pH=6,potassium phosphate buffer, and 50% saturated sodium chloride). Thisisolation of aqueous solutions to a dedicated syringe pump minimizeswater contamination throughout the rest of the machine. The argonsolenoid is used to deliver a flow of dry argon for agitating thedeprotection and for concentrating and deoxygenating the final solutionof boronic acid.

For example, deprotection at the beginning of a multistep sequencebegins with solid chiral, non-racemic PIDA boronate (1 mmol, 1 equiv)and solid sodium hydroxide (3 mmol, 3 equivs) in a 12-g Luknovacartridge. The primary pump delivers dry deoxygenated THF (10 mL, 0.1 M)to dissolve the PIDA boronate. The aqueous pump then delivers deionizedwater (3 mL, 0.33 M), creating a biphasic mixture, to dissolve thesodium hydroxide. A flow of dry argon is then delivered (in short 0.5-2second pulses) from the bottom of the tube, bubbling through andagitating the biphasic mixture for 10 minutes at which time thedeprotection is complete. Then, simultaneously the aqueous pump deliversphosphate buffer (3 mL) to quench the reaction, and the primary pumpdelivers diethyl ether (5 mL) to prepare for the separation. The aqueouspump then agitates the quenched reaction with several injections ofatmospheric air. The aqueous pump then aspirates the biphasic reactionmixture, pauses to allow full separation, and returns the remainingorganic layer to the deprotection tube. The aqueous layer is injected towaste and the aqueous pump delivers 50% saturated sodium chloride (3 mL)to the deprotection tube and agitates the mixture with severalinjections of air. Again, the aqueous pump aspirates the biphasicmixtures, pauses to allow full separation, and returns the organic layerto the deprotection tube. The aqueous layer is injected to waste.

This separation has been shown to be reproducible in the production ofaqueous layer volumes. On a 1 mmol scale the first aqueous layer is 6.0mL (±0.1 mL). On a 0.66 mmol scale the first aqueous layer is 6.2 mL(±0.1 mL). On a 0.33 mmol scale the first aqueous layer is 6.4 mL (±0.1mL). The aqueous salt volume has been shown to be 3.8 mL (±0.1 mL)regardless of reaction scale.

Subsequent deprotections begin with the purified chiral, non-racemicPIDA boronate as a solution in THF (from the automated purification)being injected into a new deprotection tube containing sodium hydroxide.The remainder of the deprotection proceeds as described above. For thesedownstream deprotections the only difference in experimental setup isthe amount of sodium hydroxide used (the stoichiometry is always 3equivalents with respect to the PIDA boronate). The solvent and reagentvolumes remain the same and are as outlined above. The separationvolumes have shown a scale dependency and are as outlined above.

The remaining manipulations (predrying, drying, and deoxygenating andconcentration) proceed as described below. The relative volumes andquantities of solvents and reagents are independent of reaction scale.

Predrying of the still-wet organic layer (ethereal solution of boronicacid) removes the bulk of the remaining water. In one embodiment, thepredrying tube is a 12-g Luknova cartridge containing a mixture ofCelite® (800 mg) and anhydrous magnesium sulfate (2.1 g). A 5-mLpolypropylene syringe plunger is placed on top of the solid mixture. Thetwo solids are mixed intimately to prevent clumping of the magnesiumsulfate clathrate. Additionally, the syringe plunger prevents movementof the solids up the tube as liquids are injected. To begin thepredrying step, the primary pump delivers 5 mL of dry deoxygenated THFto the predrying tube. It has been shown that the solids adsorbapproximately 5 mL of THF during this process, so wetting the solidswith clean THF prevents loss of volume. Next, the primary pump transfersthe organic layer from the deprotection tube into the predrying tube.The solution is passed over the solid mixture by repeatedaspiration/injection (rate=15 mL/min) via the primary pump. In total,the solution is agitated in this manner 20 times. At this point the bulkwater has been removed from the solution of boronic acid.

Drying of the ethereal boronic acid solution is required to remove theremaining residual water. In one embodiment, the drying tube is a 12-gLuknova cartridge containing a layer of Celite® (300 mg) topped withactivated molecular sieves (4 Å, −325 mesh, 3.6 g). A 5-mL polypropylenesyringe plunger is placed on top of these solids. The bottom layer ofCelite® prevents clogging of the tube frit by the fine molecular sieves.The syringe plunger prevents movement of solids as described above. Tobegin the drying step, the primary pump delivers 5 mL of drydeoxygenated THF to the predrying tube. As described above, thisprevents loss of volume. Next, the primary pump transfers the predriedsolution of boronic acid from the predrying tube to the drying tube.Similar to the agitation method described above, the solution is passedover the solids by repeated aspiration/injection (rate=5 mL/min) via theprimary pump. In total, the solution is agitated in this manner 12times. The rate of aspiration during the drying step achievesappropriate aspiration and thereby thorough agitation. Specifically, aslow aspiration rate of about 5 mL/min efficiently aspirates the boronicacid solution through the layer of molecular sieves. Faster rates resultin the build-up of vacuum that is dissipated by solvent evaporationrather than solution aspiration; boronic acid solution is notefficiently passed over the molecular sieves and remains wet. At thispoint the boronic acid solution has been thoroughly dried.

Deoxygenating the boronic acid solution is required in preparation ofthe cross-coupling reaction. Specifically, the solution needs to bedeoxygenated for the coupling to proceed productively. Additionally,concentration of the solution is useful to remove any diethyl ether thatis still present from the deprotection workup, as well as to maintain aworkable volume for the cross-coupling reaction. Workable relativevolumes for the coupling reactions have been determined to be 9 mL ofboronic acid solution for all couplings, regardless of reaction scale.As an exception, the final reaction in a sequence requires a boronicacid solution of 2 mL. In one embodiment, the concentration tube is anempty 12-g Luknova cartridge. To begin the deoxygenating/concentrationstep, the primary pump transfers the dry boronic acid solution to theconcentration tube. Then, dry argon is bubbled through the solution tosimultaneously deoxygenate and concentrate. The argon flow begins withshort 0.5 second pulses and these pulses become progressively longerover the course of 3 minutes, at which point the argon flow remains oncontinuously. This concentration process has been shown to reduce volumeat an approximate rate of 0.1 mL/min. Before concentration, the volumeis 18 mL and, therefore, approximately 90 minutes of argon flow reducesthe volume to 9 mL. The resulting dry, deoxygenated, concentratedsolution of boronic acid is suitable for addition to an anhydrouscross-coupling reaction.

The aqueous deprotection module represents a robust and predictablemethod for the automation of chiral, non-racemic PIDA boronatedeprotection reactions. These types of aqueous conditions are known towork for many sensitive boronic acids in the context of non-automatedsynthesis, and, as such, this automated deprotection is expected to workreliably for a wide range of sensitive substrates. This aqueousdeprotection module, however, differs from previously reported methodsof chiral, non-racemic PIDA boronate deprotection in several ways. Thechanges employed in the automated process relative to the procedureutilized in published solution-phase reactions include argon flowagitation and argon sparging deoxygenation/concentration, a three-stepdrying strategy, the minimization and use of specific solvent volumes,and controlled slow-rate aspiration for liquid handling.

In a non-automated chiral, non-racemic PIDA boronate deprotection,agitation of the biphasic reaction is achieved with conventionalstirring (magnetic stir bar and stirring plate). The aqueousdeprotection module of the invention utilizes argon gas flow to agitatethe deprotection reaction. As argon is passed through the frit of thedeprotection tube, the resulting bubbles provide highly efficientagitation of the biphasic system. The agitation is sufficient to achievefull conversion at room temperature in 10 min (similar to non-automatedconditions) without the use of a stir plate. Furthermore, the aqueousdeprotection module uses argon flow to sparge and concentrate theboronic acid solution. In non-automated syntheses with stable boronicacids, the acid is typically isolated as a solid and submitted to across-coupling in the presence of deoxygenated solvent. In the case ofunstable boronic acids, the acid is typically not isolated, butconcentrated to some small volume by iterative concentrations fromdeoxygenated solvent. Use of argon sparging and gas flow concentrationsimultaneously in the automated system deoxygenates the boronic acidsolution and concentrates it. This provides a coupling-ready boronicacid solution without the need to isolate a potentially unstable boronicacid.

Drying of the boronic acid solution for a non-automated synthesistypically involves drying over an anhydrous drying reagent, filtrationthrough Celite®, and subsequent washing of the drying reagent. The useof excess drying reagent can insure complete drying, and the use ofcopious solvent volumes can insure quantitative recovery. This increasedsolvent volume presents a challenge in the context of automation. Thatis, all the excess volume accumulated in the automated process wouldneed to be concentrated downstream. In order to minimize theaccumulation of solvent, which is closely connected to the dryingprocess, the automated system utilizes a cooperative three-step dryingstrategy and specific solvent volumes. The first of the three steps is a50% saturated sodium chloride extraction of the organic phase of thedeprotection reaction. This removes some bulk water from the organicphase and, as described above, does so with reproducible specificvolumes. The second of the three steps is the predrying of the boronicacid solution over anhydrous magnesium sulfate, which removes more bulkwater from the solution. The final step is the drying over molecularsieves, which removes the remaining residual water. As described above,each step uses specific predetermined solvent volumes to maintainminimized, yet reproducible solvent accumulation. This process, coupledwith the use of predetermined, minimized quantities of drying agents,maximizes drying and substrate recovery while minimizing solventaccumulation.

Another key difference between previously reported methods fornon-automated syntheses and the automated system of the invention is theuse of controlled slow-rate aspiration for liquid handling. Thedecreased aspiration rate during the drying step, as described above,has enabled efficient handling of liquids. Specifically, aspirationrates above 2 mL/min during the drying step cause a build-up of vacuumin the primary syringe pump. The vacuum is then relieved by theevaporation of solvent. As a result, the boronic acid solution is notfully aspirated and is not efficiently dried over the molecular sieves.Using a decreased aspiration rate minimizes the build-up of vacuum andallows for full aspiration of the boronic acid solution. This slow-rateaspiration approach has also been applied to the aspiration of crudecross-coupling reaction mixtures.

Specific volumes and amounts disclosed above can, of course, be scaledup or down to suit larger or smaller overall scale automated machines,respectively, provided that the scaled volumes and scaled amounts remainproportional to one another.

An Exemplary Automated Coupling Cycle. An example of one complete cycleof automated coupling proceeds as follows.

Step 1. In the deprotection module, catch and selective release-basedhydrolysis of a chiral, non-racemic PIDA boronate yields afreshly-prepared boronic acid as a solution in THF.

In this example, the deprotection of PIDA-protected organoboronic acidsvia solid-supported ammonium hydroxide reagent proceeds without the useof added bulk water, thereby avoiding the need to remove bulk waterprior to a subsequent anhydrous reactions (such as a cross-coupling). Arange of aqueous deprotection conditions in the context of the automatedsynthesis were tried but the following problems were found:

-   -   The amount of solvent required to extract the boronic acid        product depended on the identity of the boronic acid. Polar        boronic acids required much more solvent. Some boronic acids        were too polar to be effectively extracted.    -   The amount of solvent used in the extraction step would require        an additional evaporation step to obtain a reasonable        concentration.    -   Removing the large amount of water in the organic phase required        very large amounts of drying reagents that became impractical.    -   Completely removing the water introduced in the deprotection        step from the machine was very difficult from an engineering        standpoint. Residual water persisted in the tubing and syringes.

Running the deprotection reaction with solid KOH and anhydrous THF didnot proceed. Running the deprotection reaction with solid KOH and 1%water in THF was not a general solution because the two products of thedeprotection reaction, N-pinine iminodiacetic acid bis potassium saltand the boronate salt (the boronic acid reacts with KOH to produce theanionic boronate species), were both insoluble in THF and aggregated tocause the water and the THF to separate and the KOH to be sequestered,thus stalling the reaction. The use of Amberlyst A26(OH) resin solvedall of these problems. The resin is not anhydrous since it is preparedin water and is shipped damp; one can control the amount of water thatis present based on the volumes of organic solvent that are used to washthe resin. Accordingly, it is possible to produce a free-flowing resinthat contains only enough water to allow the deprotection reaction toproceed, and not so much water that the resulting reaction solutions cannot be easily dried with a small amount of molecular sieves. Further,residual water does not contaminate the equipment since bulk water isnever added to the reactions. The problem of aggregation is solvedbecause the N-methyliminodiacetic acid bis potassium salt produced inthe deprotection reaction becomes trapped within the pores of the resinand does not aggregate with unreacted KOH or water. Often the boronatesalt produced in the deprotection reaction also becomes trapped withinthe pores of the resin. Boronate salts trapped in the resin do notaggregate and do not stall the reaction. Further, this protocol is theonly deprotection condition for PIDA boronates that does not requirestirring. The reaction with Amberlyst A26(OH) proceeds to fullconversion within 60 minutes with periodic air bubbling to mix themixture, thus allowing a large number of deprotection reactions to beperformed in parallel with simple equipment. The mixture (resin and THF)is then treated with dilute acetic acid to convert the boronate salt tothe boronic acid. The very fine, very polar N-pinene iminodiacetic acidproduced in this process remains trapped in the Amberlyst resin whichgreatly facilitates filtration of the mixture. (Without the Amberlystresin sequestering the N-pinene iminodiacetic acid, the subsequentfiltration step was found to be unreliable.)

Step 2. This boronic acid solution is then transferred to thecross-coupling module where it is added slowly to a stirred reactionmixture containing the next halogen-bearing building block, a palladiumcatalyst, and a solid inorganic base. Conversion of each halide buildingblock is maximized via: (a) using excess boronic acid (˜3 equiv.)relative to halide (1 equiv.); (b) employing slow-addition orslow-release of the boronic acid to help avoid its decomposition in situduring the cross-coupling reaction; and (c) using Buchwald's highlyeffective and air-stable SPhosPd catalyst to maximize the generality,efficiency, and mild nature of the cross-coupling condition (D. M.Knapp, E. P. Gillis J. Am. Chem. Soc. 2009, 131, 6961-6963; and R.Martin S. L. Buchwald Acc. Chem. Res. 2008, 41, 1461-1473).

Step 3. The soluble components of the resulting crude reaction mixtureare transferred to the purification module where the chiral, non-racemicPIDA boronate product is purified via tandem precipitation andcatch-and-release processes, as described above.

In the automated system the THF:hexane solution, Et₂O with 1.5% MeOH(v/v) solution and Et₂O solution are withdrawn from the top of the SiO₂column and through the bottom under vacuum. This approach is differentfrom standard chromatography in which the solution is pushed through thetop of the column under pressure. Again, the unique elution propertiesof the chiral, non-racemic PIDA boronate hold up under thismodification, and this modification greatly simplifies the engineeringof the purification step. In the automated system the THF is injectedinto the bottom of the column and flows out through the top underpositive pressure. In this way the PIDA boronate, which is immobilizednear the top of the column, has the least distance to be carried in theTHF (has the smallest column volume) and thus the amount of THF used toelute the chiral, non-racemic PIDA boronate can be minimized. It isbelieved that flowing solvents in opposite directions at separate timeson the same column is not a standard chromatography practice.

This three-step cycle of deprotection, cross-coupling, and purificationis iterated until the final building block coupling step is reached. Tomaximize efficiency, the final coupling reaction in each sequence isperformed via in situ hydrolysis of the final chiral, non-racemic PIDAboronate under aqueous basic conditions. “Slow-release” cross-couplingin this context can help maximize the yield of this final couplingreaction. Similar to the approach used in peptide, oligonucleotide, andoligosaccharide coupling, if the individual building blocks containother types of protective groups, these are collectively removed usingmanually executed deprotection reactions prior to an automatedchromatographic purification of the final product.

The development of a fully automated ICC platform for small moleculesynthesis represents an important step towards increasing the efficiencyand flexibility with which small molecules can be prepared in thelaboratory. While certain types of small molecules (for example, thosepossessing many Csp²-Csp² linkages) are at present more amenable to thisapproach than others, the rapidly expanding scope of the Suzuki-Miyaurareaction, which increasingly includes Csp³ coupling partners (M. R.Netherton, G. C. Fu, Adv. Synth. Catal. 2004, 346, 1525-1532) suggestthat the potential generality of this approach is substantial. Thissynthesis apparatus stands to extend the power of small moleculesynthesis to the non-chemist and ultimately will help shift therate-limiting step in small molecule science from achieving syntheses tounderstanding function. Given that the functional capacity for smallmolecules likely extends far beyond that which is currently understoodor utilized, the developments described herein stand to have widespreadimpacts in both science and medicine.

EXEMPLIFICATION

The invention now being generally described, it will be more readilyunderstood by reference to the following, which is included merely forpurposes of illustration of certain aspects and embodiments of thepresent invention, and is not intended to limit the invention.

General Methods

Materials. Commercial reagents were purchased from Sigma-Aldrich, FisherScientific, Alfa Aesar, TCI America, or Frontier Scientific, and wereused without further purification unless otherwise noted. Solvents werepurified via passage through packed columns as described by Pangborn andcoworkers (THF, Et₂O, CH₃CN, CH₂Cl₂: dry neutral alumina; hexane,benzene, and toluene, dry neutral alumina and Q5 reactant; DMSO, DMF:activated molecular sieves). Pangborn et al. (1996) Organometallics15:1518-20. All water was deionized prior to use. Triethylamine,diisopropylamine, diethylamine, pyridine, 2,6-lutidine, and ethanol werefreshly distilled under an atmosphere of nitrogen from CaH₂.

General Experimental Procedures. Unless noted, all reactions wereperformed in flame-dried round-bottom or modified Schlenk flasks fittedwith rubber septa under a positive pressure of argon. Organic solutionswere concentrated via rotary evaporation under reduced pressure with abath temperature of 23° C. unless otherwise noted. Reactions weremonitored by analytical thin layer chromatography (TLC) performed usingthe indicated solvent on E. Merck silica gel 60 F254 plates (0.25 mm).Compounds were visualized by exposure to a UV lamp (λ=254 nm), and/or asolution of KMnO₄, followed by brief heating using a Varitemp heat gun.Column chromatography was performed using Merck silica gel grade 9385 60Å (230-400 mesh).

Structural analysis. ¹H NMR and ¹³C NMR spectra were recorded at 20° C.on a Varian Unity 500 instrument. Chemical shifts (δ) are reported inparts per million (ppm) downfield from tetramethylsilane and referencedto residual protium in the NMR solvent (CHCl₃, δ=7.26; acetone, 8=2.05,center line; 1,1,2,2-tetrachloroethane, 5.95) or to addedtetramethylsilane (8=0.00). Data are reported as follows: chemicalshift, multiplicity (s=singlet, d=doublet, t=triplet, q=quartet,quint=quintet, sept=septet, m=multiplet, b=broad, app=apparent),coupling constant (J) in Hertz (Hz), and integration. Chemical shifts(δ) for ¹³C NMR are reported in ppm downfield from tetramethylsilane andreferenced to carbon resonances in the NMR solvent (CDCl₃, δ=77.0,center line; acetone, δ=39.5, center line). Carbons bearing boronsubstituents were not observed (quadrupolar relaxation). 113 NMR wererecorded using a Unity Inova 400 instrument and referenced to anexternal standard of (BF₃.Et₂O).

Example 1 Pinene-Derived Iminodiacetic Acid (PIDA) is a Powerful Ligandfor Stereoselective Synthesis of Csp³ Boronate Building Blocks

The remarkable stability of the MIDA boronate motif to a wide range ofcommon reaction conditions enables the transformation of simpleboron-containing starting materials into many types of complex boronatebuilding blocks. Crystal structures of many MIDA boronates have revealedthat the N-methyl substituent is always closely positioned to theorganic group appended to the boron atom, and variable temperature NMRstudies have demonstrated that the iminodiacetic acid framework isconformationally rigid in solution.

We hypothesized that if the N-alkyl substituent of iminodiacetic acidwere chiral, then highly effective transfer of stereochemicalinformation might be achieved during functionalizations of thecorresponding boronates due to enforced proximity (FIG. 1). Given theexceptional versatility of epoxides in the preparation of other chiralbuilding blocks, we first questioned whether the epoxidation of alkenylboronates could be rendered asymmetric via such modifications of theMIDA ligand.

A range of iminodiacetic acid ligands derived from different chiralamines were surveyed, leading to the discovery that ligand 1a (PIDA; seeTable 1), which can be easily prepared from (+)-□-pinene (Brown et al.(1983) J Am Chem Soc 105:2092-3; Rathke et al. (1988) Coll Vol 6:943),is exceptionally effective. Specifically, treatment of the correspondingstyrenyl chiral, non-racemic PIDA boronate 2a with meta-chloroperbenzoicacid (mCPBA) under standard conditions yielded oxiranyl chiral,non-racemic PIDA boronate 3a with outstanding diastereoselectivity(Table 1, entry 1). Alternatively linking the pinene-derived appendagevia a conformationally-flexible methylene spacer (1b) or employing someother less-sterically bulky chiral secondary amines (1c or 1d) alsoyielded some, albeit reduced, diastereoselectivity (Table 1, entries2-4).

TABLE 1 Diastereoselective epoxidations of various iminodiaceticacid-based alkenyl boronates.

en- try 1 3 d.r.^(a) 1

>20:1 2

 21:1 3

 27:1 4

 16:1 ^(a)d.r. = diastereomeric ratio as determined via 500 MHz ¹H NMRanalysis of unpurified reaction mixture.

Single crystal X-ray analysis of 3a (Table 1, entry 1) revealed that,despite N-alkylation with a very sterically bulky substituent, the[3.3.0]-bicyclic structure of the iminodiacetic acid motif is preservedand the chiral alkyl group is positioned<2.4 Å from the newly formedepoxide. Moreover, variable-temperature NMR analysis confirmed that theiminodiacetic acid framework of the PIDA ligand is conformationallyrigid for both the starting material 2a and product 3a. Collectively,these findings are consistent with the conclusion that highly effectivetransfer of stereochemical information in this system is attributable toenforced proximity between the chiral appendage and the site ofreactivity during the transition state of the epoxidation reaction.

The capacity of PIDA to enable the diastereoselective epoxidation of avariety of alkenyl boronates was explored. As shown in Table 2, theepoxidation of a series of 1,2-disubstituted olefins 2a-g were allefficiently epoxidized in good yields and with outstanding stereocontrol(entries 1-4). 2a can also be epoxidized on a 15 mmol scale and isolatedvia simple crystallization (entry 1). Strikingly, even the smallestolefin, vinyl boronate 2 h, was epoxidized with outstandingdiastereoselectivity (entry 5). All of these streochemically pureoxiranyl PIDA boronates 3 are crystalline free-flowing solids that arecompletely stable to silica gel chromatography and bench-top storageunder air, making them highly desirable building blocks for manyapplications in complex molecule synthesis.

TABLE 2 Highly diastereoselective epoxidations with PIDA boronates.

entry 2 3 % yield^(a,b) d.r.^(c) 1d

53 (65)^(d) >20:1 2 

64 >20:1 3 

77 >20:1 4 

75 >20:1 5 

82 >20:1 ^(a)Isolated yields after silica gel chromatography. ^(b)Thestereochemistry of epoxides 3a, 3e, and 3h were all determinedunambiguously via single crystal X-ray analysis. Remaining productconfigurations were assigned by analogy. ^(c)d.r. = diastereomeric ratioas determined via 500 MHz ¹H NMR analysis of unpurified reactionmixtures. ^(d)Conducted on a 15 mmol scale and isolated bycrystallization. Ipc = isopinocamphenyl.

Example 2 General Procedure for the Synthesis of Ligands 1a-d

To a stirred solution of chloroacetic acid (69 mmol, 2.3 equiv) in H₂O(60 mL) at 0° C. was added dropwise 5 N NaOH solution (13.8 mL, 69 mmol,2.3 equiv), keeping the temperature below 15° C. The amine (30 mmol, 1equiv) in IPA (30 mL) was then added in one portion. The ice bath wasthen removed and the reaction heated at 70° C. (oil bath temperature).After stirring for 2.5 h, the reaction turned clear from an initialbiphasic mixture. Another 8.1 mL (40.5 mmol, 1.35 equiv) of the 5 N NaOHsolution was added, and the reaction stirred for a further 14 h at thesame temperature. The third portion of the NaOH solution (8.1 mL, 40.5mmol, 1.35 equiv) was then added and stirred for an additional 2 h at70° C. The reaction was then heated up to 100° C. BaCl₂.H₂O (7.69 g,31.5 mmol, 1.05 equiv) in H₂O (30 mL) was heated until the soliddissolved completely. This heated solution was then added dropwise viapipette into the reaction mixture. After the addition, the reaction wasstirred for an additional 15 min, during which the reaction became athick white suspension. After cooling to room temperature, the whitesolid was collected by filtration and dried in a vacuum oven set at 100°C. The mass of the Ba chelate was determined. The Ba chelate was thensuspended in H₂O (60 mL) and heated in a 110° C. oil bath until boiling.5M H₂SO₄ (1.95 equiv relative to the Ba chelate) was added dropwise,followed by rinsing with 5 mL H₂O. The resulting suspension was stirredfor another 15 min in the oil bath, then cooled for 5 min and filteredthrough Celite, rinsing with 10 mL H₂O. The filtrate was concentrated todryness. The solid obtained was then redissolved in Et₂O/CH₂Cl₂ (1:10,100 mL) and filtered to remove insoluble solids. The CH₂Cl₂ solution wasthen concentrated in vacuo and the solid obtained was used withoutfurther purification.

Ligand 1a. The general procedure was followed using(1R,2R,3R,5S)-(−)-Isopinocampheylamine (4.59 g, 30 mmol), chloroaceticacid (6.52 g, 69 mmol) and NaOH (30 mL, 150 mmol). 11.33 g of the Bachelate (93%) was obtained. 5.4 mL of 5M H₂SO₄ was used for thehydrolysis, and the ligand 1a was obtained as an off-white solid (6.63g, 82%). ¹H NMR (500 MHz, DMSO-d₆) δ 3.45 (s, 4H), 3.23-3.18 (m, 1H),2.32-2.23 (m, 1H), 2.19-2.12 (m, 1H), 1.91-1.86 (m, 1H), 1.75-1.69 (m,2H), 1.64-1.60 (m, 1H), 1.15 (s, 3H), 1.03 (d, J=6.5, 3H), 0.92 (s, 3H),0.79 (d, J=10 Hz, 1H); ¹³C NMR (125 MHz, DMSO-d₆) δ 173.5, 62.0, 53.8,47.3, 40.9, 40.3, 38.7, 33.4, 29.6, 27.9, 23.0, 20.9; HRMS (ESI+)Calculated for C₁₄H₂₄NO₄: 270.1705, Found: 270.1703.

Ligand 1b. The general procedure was followed using(−)-cis-myrtanylamine (4.59 g, 30 mmol), chloroacetic acid (6.52 g, 69mmol) and NaOH (30 mL, 150 mmol). 11.33 g of the Ba chelate (93%) wasobtained. 5.4 mL of 5M H₂SO₄ was used for the hydrolysis, and the ligand1b was obtained as an off-white solid in about 70-80% purity (1.62 g,20%). ¹H NMR (500 MHz, DMSO-d₆) δ 3.38 (s, 4H), 2.56 (d, J=7.5 Hz, 2H),2.51-2.42 (m, 1H), 2.30-2.26 (m, 1H), 22.1-2.06 (m, 1H), 1.94-1.72 (m,5H, 1.53-1.45 (m, 1H), 1.12 (s, 3H), 0.91 (s, 3H); ¹³C NMR (125 MHz,DMSO-d₆) δ 172.5, 59.6, 55.4, 43.4, 40.9, 38.6, 38.2, 32.9, 27.8, 25.8,22.9, 19.5; HRMS (ESI+) Calculated for C₁₄H₂₄NO₄: 270.1705, Found:270.1700.

Ligand 1c. The general procedure was followed using(S)-(+)-1-cyclohexylethylamine (12.72 g, 100 mmol), chloroacetic acid(21.74 g, 230 mmol) and NaOH (100 mL, 500 mmol). 27.84 g of the Bachelate (74%) was obtained. 14.4 mL of 5M H₂SO₄ was used for thehydrolysis, and the ligand 1c was obtained as an off-white solid (12.47g, 51%). ¹H NMR (500 MHz, DMSO-d₆) δ 3.37 (d, J=17.5 Hz, 2H), 3.29 (d,J=17.5 Hz, 2H), 2.39 (m, 1H), 1.91 (app d, J=7.5 Hz, 1H), 1.65-1.51 (m,4H), 1.24-1.03 (m, 5H), 0.92 (d, J=6.5 Hz, 3H), 0.89-0.78 (m, 1H); ¹³CNMR (125 MHz, DMSO-d₆) δ 173.4, 62.6, 53.2, 40.8, 30.0, 29.4, 26.1,25.8, 25.8, 12.6; HRMS (ESI+) Calculated for C₁₂H₂₂NO₄: 244.1550, Found:244.1549.

Ligand 1d. The general procedure was followed using (1S,2S)-(+)-2-benzyloxycyclopentylamine (5 g, 26.1 mmol), chloroacetic acid(5.68 g, 60.1 mmol) and NaOH (26.1 mL, 130.5 mmol). 5.87 g of the Bachelate (67%) was obtained. 3.40 mL of 5M H₂SO₄ was used for thehydrolysis, and the ligand 1d was obtained as an off-white solid (3.36g, 42%). ¹H NMR (500 MHz, DMSO-d₆) δ 12.2 (br s, 2H), 7.32-7.24 (m, 5H),4.42 (d, J=12 Hz, 1H), 4.36 (d, J=11.5 Hz, 1H), 3.76-3.74 (m, 1H), 3.48(d, J=17.5 Hz, 2H), 3.43 (d, J=18 Hz, 2H), 3.24-3.20 (m, 1H), 1.88-1.82(m, 1H), 1.82-1.76 (m, 1H), 1.59-1.48 (m, 3H), 1.38-1.30 (m, 1H); ¹³CNMR (125 MHz, DMSO-d₆) δ 173.0, 138.6, 128.1, 127.6, 127.3, 83.0, 70.4,68.1, 53.6, 29.8, 28.4, 20.9; HRMS (ESI+) Calculated for C₁₆H₂₂NO₅:308.1498, Found: 308.1493.

Example 3 General Procedure for the Complexation of Chiral Ligands 1a-dto trans-2-Phenylvinylboronic Acid

To a solution of trans-2-phenylvinylboronic acid (1.5 equiv) in toluene(30 mL) and DMSO (1.5 mL) was added the ligand 1 (typically 1-5 mmol, 1equiv). The flask was fitted with a Dean-Stark trap. The Dean-Stark trapwas fitted with an air-cooled condenser vented to ambient atmosphere.The stirred solution was refluxed with azeotropic removal of water for 2h. The toluene was removed in vacuo, and the residue was taken up in 2:1EtOAc/acetone (60 mL) and washed twice with 1:1 brine/H₂O (30 mL). Theaqueous layer was extracted with 2:1 EtOAc/acetone (30 mL) and thecombined organic phase washed with brine, dried over MgSO₄, filtered andconcentrated in vacuo. The crude product was then purified by silica gelchromatography, eluting first with Et₂O to remove impurities, then with1:4 (acetone/Et₂O).

Boronate ester 2a. The reaction was carried out on a 20 mmol scale withsome modifications from the general procedure and purified without theuse of silica gel chromatography: To a suspension oftrans-2-phenylvinylboronic acid (2.96 g, 20 mmol) in toluene (200 mL)was added the ligand 1a (9.68 g, 36 mmol). The flask was fitted with a50 mL Dean-Stark trap and an air-cooled condenser vented to ambientatmosphere. The stirred solution was refluxed with azeotropic removal ofwater for 2 h. After cooling to room temperature, the crude solidproduct was collected via vacuum filtration. The filtrate was thenconcentrated to dryness and Et₂O (50 mL) was added. The resulting whiteprecipitate was collected via vacuum filtration and the combined solidswere then washed with additional Et₂O (50 mL). This solid was then takenup in acetone (150 mL) and passed slowly through a pad of silica gel ina 100 mL sintered funnel, eluting with additional acetone (50 mL). Thefiltrate thus obtained was concentrated and dried in vacuo, giving theproduct (6.74 g, 88%).

Results: TLC (Hexanes:acetone 3:2) R_(f)=0.27, visualized by short waveUV; NMR (500 MHz, acetone-d₆) δ 7.54-7.53 (m, 2H), 7.37-7.33 (m, 2H),7.29-7.25 (m, 1H), 7.03, (d, J=18 Hz, 1H), 6.52 (d, J=18 Hz, 1H), 4.35(d, J=16 Hz, 1H), 4.29 (d, J=17.5 Hz, 1H), 4.18 (d, J=15.5 Hz, 1H), 4.05(d, J=18 Hz, 1H), 4.05-4.00 (m, 1H), 2.65-2.58 (m, 1H), 2.52-2.48 (m,1H), 2.46-2.41 (m, 1H), 2.01-1.99 (m, 1H), 1.91 (dt, J=6, 2.5 Hz, 1H),1.71 (ddd, J=15, 6.5, 2.5 Hz, 1H), 1.35 (d, J=6.5 Hz, 3H), 1.23 (s, 3H),1.08 (d, J=10.5 hz, 1H), 0.92 (s, 3H); ¹³C NMR (125 MHz, acetone-d₆) δ170.8, 167.9, 143.5, 139.3, 129.4, 128.8, 127.4, 68.6, 61.1, 55.3, 50.2,41.6, 39.6, 39.2, 32.4, 31.1, 27.4, 23.6, 23.5; ¹¹B-NMR (100 MHz,acetone-d₆) δ 11.9; HRMS (ESI+) Calculated for C₂₂H₂₉BNO₄: 382.2190,Found: 382.2187.

Boronate ester 2b. The general procedure was followed usingtrans-2-phenylvinylboronic acid (0.22 g, 1.5 mmol), ligand 1b (0.606 g,2.25 mmol) in 20 mL toluene and 1 mL DMSO. A white solid was obtained(0.387 g, 68%). TLC (Hexanes:EtOAc:Et₂O 2:2:1) R_(f)=0.20, visualized byshort wave UV; ¹H NMR (500 MHz, acetone-d₆) δ 7.50 (app d, J=7 Hz, 2H),7.34 (app t, J=7.5 Hz, 2H), 7.28-7.25 (m, 1H), 6.93, (d, J=18 Hz, 1H),6.33 (d, J=18 Hz, 1H), 4.17-4.08 (m, 4H), 3.45 (dd, J=13.5, 6.5 Hz, 1H),3.34 (dd, J=13.5, 3 Hz, 1H), 2.74-2.68 (m, 1H), 2.38-2.26 (m, 2H),2.16-2.11 (m, 1H), 2.01-1.94 (m, 1H), 1.92-1.76 (m, 3H), 1.15 (s, 3H),1.08 (d, J=10 Hz, 1H), 0.92 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ 167.8,167.4, 144.2, 137.6, 128.6, 128.4, 126.7, 66.8, 58.5, 58.4, 47.3, 40.4,38.1, 37.4, 31.9, 27.3, 25.6, 23.3 (2C); ¹¹B-NMR (100 MHz, acetone-d₆) δ11.9; HRMS (ESI+) Calculated for C₂₂H₂₉BNO₄: 382.2190, Found: 382.2187.

Boronate ester 2c. The general procedure was followed usingtrans-2-phenylvinylboronic acid (0.74 g, 5 mmol), ligand 1c (1.82 g, 7.5mmol) in 50 mL toluene and 2.5 mL DMSO. A white solid was obtained(0.311 g, 74%). TLC (Hexanes:acetone 3:2) R_(f)=0.38; ¹H NMR (500 MHz,acetone-d₆) δ 7.52 (d, J=8 Hz, 2H), 7.35 (t, J=7.5 Hz, 2H), 7.27 (t,J=7.5 Hz, 1H), 6.96, (d, J=18 Hz, 1H), 6.46 (d, J=18 Hz, 1H), 4.27 (d,J=17 Hz, 1H), 4.19 (d, J=17 Hz, 1H), 4.05 (d, J=14.5 Hz, 1H), 4.02 (d,J=17 Hz, 1H), 3.42-3.38 (m, 1H), 2.05 (m, 1H), 1.86-1.83 (m, 1H),1.78-1.74 (m, 1H), 1.69-1.62 (m, 2H), 1.50-1.44 (m, 1H), 1.36-1.27 (m,6H), 1.18-1.08 (m, 2H); ¹³C NMR (125 MHz, CDCl₃) δ 168.5, 167.7, 144.3,128.6, 128.4, 126.7, 67.6, 56.8, 39.2, 32.1, 27.7, 26.4, 25.7, 25.7,10.5; ¹¹B-NMR (100 MHz, acetone-d₆) δ 11.9; HRMS (ESI+) Calculated forC₂₀H₂₇BNO₅: 356.2033, Found: 356.2029.

Boronate ester 2d. The general procedure was followed usingtrans-2-phenylvinylboronic acid (0.148 g, 1 mmol), ligand 1d (0.461 g,1.5 mmol) in 15 mL toluene and 0.5 mL DMSO. An off-white solid wasobtained (0.311 g, 74%). TLC (Hexanes:acetone 3:2) R_(f)=0.38; ¹H NMR(500 MHz, acetone-d₆) δ 7.50 (d, J=8 Hz, 2H), 7.38-7.29 (m, 6H),7.26-7.22 (m, 1H), 7.18-7.13, (m, 1H), 6.96 (d, J=18 Hz, 1H), 6.46 (d,J=18.5 Hz, 1H), 4.62 (d, J=11.5 Hz, 1H), 4.55 (d, J=11 Hz, 1H),4.41-4.38 (m, 1H), 4.29 (d, J=16.5 Hz, 1H), 4.19 (d, J=17.5 Hz, 1H),4.14 (d, J=16.5 Hz, 1H), 4.05 (d, J=17 Hz, 1H), 3.70 (q, J=9 Hz, 1H),2.30-2.25 (m, 1H), 2.20-2.15 (m, 1H), 1.82-1.6 (m, 4H); ¹³C NMR (125MHz, CDCl₃) δ 168.8, 167.5, 144.3, 137.5, 136.4, 128.8, 128.6, 128.5,128.4, 128.3, 126.8, 79.3, 73.4, 72.0, 60.0, 55.4, 29.6, 26.2, 21.1;¹¹B-NMR (100 MHz, acetone-d₆) δ 11.8; HRMS (ESI+) Calculated forC₂₄H₂₇BNO₅: 420.1978, Found: 420.1982.

Example 4 Synthesis of Boronate Ester 2e

To a solution of S-2 (197 mg, 1 mmol) in THF (10 mL) was added 1N NaOH(3 mL, 3 mmol) under ambient atmosphere and temperature and stirredvigorously for 15 min. The reaction was quenched with the addition ofsat. NH₄Cl solution (10 mL). The mixture was stirred for 3 min, thentransferred to a separatory funnel, rinsing with Et₂O (10 mL). Afterphase separation, the organic phase was washed with another portion ofsat. NH₄Cl solution (10 mL) and the combined aqueous phase extractedwith 1:1 THF/Et₂O (15 mL). The organic phase was dried over MgSO₄,filtered and concentrated in vacuo to give the boronic acid as a whitesolid. The solid was taken up in toluene (15 mL) and DMSO (0.75 mL) and1a (404 mg, 1.5 mmol) was added. The reaction was heated to reflux witha Dean-Stark trap for 1.5 h. After cooling to room temperature, toluenewas removed in vacuo. The residue was taken up in 2:1 EtOAc/acetone (15mL) and washed twice with 1:1 H₂O/brine (10 mL). The aqueous layers wereextracted with 2:1 EtOAc/acetone (15 mL). The combined organic phase wasdried over MgSO₄, filtered and concentrated. The crude product waspurified by silica gel chromatography, eluting first with Et₂O then with1:4 acetone/Et₂O to give a white solid as the pure product (166 mg, 52%over 2 steps).

Results. TLC (Hexanes:acetone 3:2) R_(f)=0.41, stained by KMnO₄; ¹H NMR(500 MHz, acetone-d₆) δ 6.13 (dq, J=8.5 Hz, 1H), 5.66 (dd, J=17.5, 1.5Hz, 1H), 4.19 (d, J=18 Hz, 1H), 4.18 (d, J=16 Hz, 1H), 4.09 (d, J=15.5Hz, 1H), 3.94 (d, J=18 Hz, 1H), 3.87 (dt, J=10, 3 Hz, 1H), 2.57-2.51 (m,1H), 2.49-2.42 (m, 2H), 2.00 (sept, J=3 Hz, 1H), 1.91 (dt, J=6, 2 Hz,1H), 1.79 (dd, J=6.5, 1.5 Hz, 3H), 1.61 (ddd, J=15, 6.5, 1.5 Hz, 1H),1.33 (d, J=7 Hz, 3H), 1.25 (s, 3H), 1.04 (d, J=10.5 Hz, 1H), 0.98 (s,3H); ¹³C NMR (125 MHz, acetone-d₆) δ 170.2, 167.2, 140.8, 67.9, 60.3,54.5, 49.6, 41.0, 39.0, 38.5, 31.8, 30.3, 26.9, 23.0, 22.9, 20.8;¹¹B-NMR (100 MHz, acetone-d₆) δ 11.5; HRMS (ESI+) Calculated forC₁₇H₂₇BNO₄: 320.2033, Found: 320.2035.

Example 5 Synthesis of Boronate Ester 2 g

In an unoptimized procedure, TBS-protected propargyl alcohol (5.17 g,30.4 mmol) was weighed into a dry 20 mL Ichem vial and the vial wassealed with a septum cap. The vial was flushed with N₂ for 20 min, thencatecholborane (3.4 mL, 31.9 mmol) was added neat in one portion. Thereaction was stirred at 60° C. in a heating block for 15 h. Aftercooling to room temperature, 4.36 g (approx. 15 mmol) of this crudeproduct was diluted in THF (150 mL) and 1 N NaOH (45 mL, 45 mmol) wasadded. After vigorous stirring for 10 min, the mixture was transferredto a separatory funnel and the phases separated. The organic layer waswashed with 1 N NaOH (60 mL), then H₂O (60 mL) and 1:1 H₂O/brine (60mL). The organic phase was then dried over MgSO₄, filtered andconcentrated to give a yellow oil as the boronic acid (1.48 g, 6.85mmol). The boronic acid was then dissolved in toluene (60 mL) and DMSO(3 mL). Ligand 1a was then added, and the mixture was heated to refluxwith a Dean-Stark trap for 2 h. The reaction was then cooled to roomtemperature. Toluene was then removed in vacuo. Et₂O was added to theresidue and the precipitate, which is the crude product, was obtained byvacuum filtration. Purification by silica gel chromatography (30-100%EtOAc/hexane) gave a white solid (405 mg, ˜30% from boronic acid).

Results. TLC (Hexanes: acetone 3:2) R_(f)=0.51 visualized by KMnO₄; ¹HNMR (500 MHz, CDCl₃) δ 6.22 (dt, J=17.5, 4 Hz, 1H), 5.94 (dt, J=17.5, 2Hz, 1H), 4.26-4.25 (m, 2H), 4.23 (d, J=18 Hz, 1H), 4.18 (d, J=15.5 Hz,1H), 4.12 (d, J=15 Hz, 1H), 3.98 (d, J=18 Hz, 1H), 3.86 (dt, J=10.5, 6Hz, 1H), 2.59-2.53 (m, 1H), 2.49-2.41 (m, 2H), 1.99 (sept, J=3 Hz, 1H),1.92 (dt, J=6, 2 Hz, 1H), 1.66 (ddd, J=15, 6.5, Hz, 1H), 1.34 (d, J=7Hz, 3H), 1.25 (s, 3H), 1.07 (d, J=10.5 Hz, 1H), 0.99 (s, 3H), 0.9 (s,9H), 0.1 (s, 6H); ¹³C NMR (125 MHz, CDCl₃) δ 169.7, 167.0, 146.2, 68.4,64.3, 60.3, 54.2, 49.0, 40.6, 38.9, 38.8, 32.0, 30.8, 30.2, 27.0, 25.9,23.5 (2C), 15.2, −5.4; ¹¹B-NMR (100 MHz, acetone-d₆) δ 11.8; HRMS (ESI+)Calculated for C₂₃R₄₁BNO₅Si: 450.2847, Found: 450.2845.

Example 6 Synthesis of Boronate Ester 2f

The boronate ester 2 g (1.52 g, 3.38 mmol) was dissolved in CH₂Cl₂ (68mL) and cooled to 0° C. H₂O (0.34 mL) followed by TFA (6.80 mL) was thenadded. The reaction was stirred at 0° C. for 30 min. The reaction waswashed briefly with H₂O (30 mL), then twice with sat. aqueous NaHCO₃ (30mL). The combined aqueous layer was washed with CH₂Cl₂ (30 mL). Theorganic phase was then dried over MgSO₄, filtered and concentrated.Following purification by silica gel chromatography (40480%EtOAc/hexane), a white solid was obtained (737 mg, 65%).

Results. TLC (Hexanes:acetone 3:2) R_(f)=0.20, visualized by KMnO₄; ¹HNMR (500 MHz, acetone-d₆) δ 6.26 (dt, J=18, 4 Hz, 1H), 5.89 (app d,J=17.5 Hz, 1H), 4.12 (d, J=15 Hz, 1H), 4.12 (m, 2H), 3.89 (dt, J=10, 6.5Hz, 1H), 2.56 (m, 1H), 2.48-2.2 (m, 2H), 1.99 (sept, J=3 Hz, 1H), 1.91(dt, J=6, 2.5 Hz, 1H), 1.63 (ddd, J=15, 6.5, 5 Hz, 1H), 1.35 (d, J=7 Hz,3H), 1.25 (s, 3H), 1.06 (d, J=10.5 Hz, 1H), 0.97 (s, 3H); ¹³C NMR (125MHz, acetone-d₆) δ 170.8, 167.9, 146.5, 68.5, 64.5, 60.9, 55.2, 50.2,41.6, 39.6, 39.1, 32.3, 30.9, 27.5, 23.6, 23.6; ¹¹B-NMR (100 MHz,acetone-d₆) δ 11.8; HRMS (ESI+) Calculated for C₁₇H₂₇BNO₅: 336.1982,Found: 336.1979.

Example 7 Synthesis of Boronate Ester 2 h

To a solution of S-6 (183 mg, 1 mmol) (Sigma-Aldrich product no. 704415)in THF (10 mL) was added 1 N NaOH (3 mL, 3 mmol) under ambientatmosphere and temperature and stirred vigorously for 15 min. Thereaction was quenched with the addition of sat. NH₄Cl solution (10 mL).The mixture was stirred for 3 min, then transferred to a separatoryfunnel, rinsing with Et₂O (10 mL). After phase separation, the organicphase was washed with another portion of sat. NH₄Cl solution (10 mL) andthe combined aqueous phase extracted with 1:1 THF/Et₂O (15 mL). Theorganic phase was dried over MgSO₄, filtered and concentrated in vacuoto give the boronic acid as a white solid. The solid was taken up intoluene (15 mL) and DMSO (0.75 mL) and 1a (404 mg, 1.5 mmol) was added.The reaction was heated to reflux with a Dean-Stark trap for 1.5 h.After cooling to room temperature, toluene was removed in vacuo. Theresidue was taken up in 2:1 EtOAc/acetone (15 mL) and washed twice with1:1 H₂O/brine (10 mL). The aqueous layers were extracted with 2:1EtOAc/acetone (15 mL). The combined organic phase was dried over MgSO₄,filtered and concentrated. The crude product was purified by silica gelchromatography, eluting first with Et₂O then with 1:4 acetone/Et₂O togive a white solid as the pure product (153 mg, 55% over 2 steps).

Results. TLC (Hexanes:acetone 3:2) R_(f)=0.39, visualized by KMnO₄; ¹HNMR (500 MHz, acetone-d₆) δ 6.15 (dd, J=19, 13.5 Hz, 1H), 5.78 (app d,J=12.5 Hz, 1H), 5.73 (dd, J=19, 3.5 Hz, 1H), 4.24 (d, J=18 Hz, 1H), 4.23(d, J=15.5 Hz, 1H), 4.14 (d, J=15.5 Hz, 1H), 4.00 (d, J=18 Hz, 1H), 3.90(dt, J=10, 6.5 Hz, 1H), 2.58-2.52 (m, 1H), 2.50-2.41 (m, 2H), 2.00(sept, J=3.5 Hz, 1H), 1.92 (ddd, J=6, 6, 2 Hz, 1H), 1.63 (ddd, J=15, 6,2.5 Hz, 1H), 1.35 (d, J=7 Hz, 3H), 1.25 (s, 3H), 1.06 (d, J=10 Hz, 1H),0.98 (s, 1H); ¹³C NMR (125 MHz, acetone-d₆) δ 170.2, 167.8, 130.1, 68.6,61.0, 55.2, 50.2, 41.6, 39.6, 39.2, 32.3, 31.0, 27.4, 23.6; ¹¹B-NMR (100MHz, acetone-d₆) δ 11.3; HRMS (ESI+) Calculated for C₁₆H₂₅BNO₄:306.1877, Found: 306.1872.

Example 8 General Procedure for the Epoxidation of Boronate Esters 2a-d(Table 1)

To a solution of the boronate ester 2 (0.1 mmol) in CH₂Cl₂ at 0° C. wasadded meta-chloroperbenzoic acid (mCPBA) (max 77%, 43 mg, 0.19 mmol)portionwise over 3 min under ambient atmosphere. The reaction wasstirred for 12 h, gradually raising the temperature to 23° C. Thereaction was then concentrated in vacuo at 20° C., and ¹H NMR analysiswas carried out. Conversions for all 4 substrates (2a-d) was >95%. Thepeaks from the protons on the epoxide were used to determine the d.r.See Table 1 (Example 1) for more details.

Epoxide 3a. The general procedure was followed using boronate ester 2a(38 mg, 0.1 mmol) and mCPBA (43 mg, 0.19 mmol). d.r.>20:1.

Results. TLC (Hexanes:acetone 3:2) R_(f)=0.46, visualized by KMnO₄; ¹HNMR (500 MHz, CDCl₃) δ 7.40-7.35 (m, 4H), 7.33-7.30 (m, 1H), 4.40 (dt,J=10.5, 3.5 Hz, 1H), 4.36 (d, J=18 Hz, 1H), 4.22 (d, J=15 Hz, 1H), 4.14(d, J=17.5 Hz, 1H), 4.12 (d, J=17.5 Hz, 1H), 3.83 (d, J=2.5 Hz, 1H),2.92-2.86 (m, 1H), 2.62-2.57 (m, 1H), 2.57 (d, J=2.5 Hz, 1H), 2.53-2.47(m, 1H), 2.11-2.08 (m, 1H), 2.00 (dt, J=5.5, 2 Hz, 1H), 1.85 (ddd,J=14.5, 4, 2.5 Hz, 1H), 1.45 (d, J=6.5 Hz, 3H), 1.31 (s, 3H), 1.14 (d,J=11 Hz, 1H), 1.10 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ 169.1, 166.4,137.9, 128.5, 128.1, 125.5, 68.1, 61.8, 56.7, 54.7, 49.0, 40.6, 39.2,39.0, 32.1, 30.6, 27.1, 23.5, 23.5; ¹¹B-NMR (128 MHz, CDCl₃) δ 10.5;HRMS (ESI+) Calculated for C₂₂H₂₉BNO₅: 398.2139, Found: 398.2135.

Epoxide 3b. The general procedure was followed using boronate ester 2b(38 mg, 0.1 mmol) and mCPBA (43 mg, 0.19 mmol). d.r.=1.86:1.

Epoxide 3c. The general procedure was followed using boronate ester 2c(36 mg, 0.1 mmol) and mCPBA (43 mg, 0.19 mmol). d.r.=2.7:1.

Epoxide 3d. The general procedure was followed using boronate ester 2d(42 mg, 0.1 mmol) and mCPBA (43 mg, 0.19 mmol). d.r.=1.56:1

Example 9 General Procedure for the Epoxidation of Boronate Esters 2a,2e-h (Table 2)

To a solution of the boronate ester 2 (0.25 mmol) in CH₂Cl₂ at 0° C. wasadded mCPBA (max 77%, 106 mg, 0.475 mmol) portionwise over 3 min underambient atmosphere. The reaction was stirred for 12 h, gradually raisingthe temperature to rt in the ice/water bath. The reaction was thenconcentrated in vacuo at 20° C., and ¹H NMR analysis of the crudereaction mixture was performed to determine the d.r. The crude productwas then taken up in a minimum amount of CH₂Cl₂ and loaded onto a silicagel column equilibrated with 30% Et₂O/hexane. The non-polar impuritieswere eluted with 30% Et₂O/hexane. The product was then eluted with 2:2:6(acetone/Et₂O/hexane). After concentration at room temperature, thesolid was washed with Et₂O (10-20 mL) to remove residual mCPBA andvacuum filtered. The epoxide was then dried in vacuo.

Epoxide 3a. The general procedure was followed using boronate ester 2a(95 mg, 0.25 mmol) and mCPBA (106 mg, 0.475 mmol), giving the product asa white solid (53 mg, 53%). d.r.>20:1. X-ray quality crystals wereobtained by making a saturated solution of 3a in 1 mL of1,2-dichloroethane and layering it with about 2 mL of hexane. The layerswere allowed to slowly mix at room temperature, giving the desiredcrystals.

The epoxidation of 2a was also carried out on a 15 mmol scale asfollows: A solution of boronate ester 2a (5.72 g, 15 mmol) in CH₂Cl₂(300 mL) was cooled to 0° C. mCPBA (max 77%, 4.47 g, 20 mmol) was addedportionwise under ambient atmosphere over 10 min. The reaction wasstirred for 8 h, maintaining the bath temperature at 0-10° C. Thereaction was then concentrated to approximately 50 mL of CH₂Cl₂, andEt₂O was added (150 mL). The solution was stirred vigorously for 5 min,and the white solid (crude product) formed was obtained by vacuumfiltration. The filtrate was concentrated to approximately 20 mL ofCH₂Cl₂ and Et₂O (100 mL) and hexane (50 mL) was added. The white solidformed was collected by vacuum filtration. The filtrate, containingmostly mCPBA, m-chlorobenzoic acid and other non-polar impurities, wasdiscarded. The combined white solid was dissolved in a minimum amount ofCH₂Cl₂ in a 250 mL Erlenmeyer flask and layered with hexane(CH₂Cl₂:hexane 1:2). The flask was then cooled to −20° C. in a freezer.This recrystallized product was then collected by vacuum filtration andwashed with CH₂Cl₂/hexane 1:10. The white solid was then dried in vacuo(3.87 g, 65%). Spectral data are identical to that obtained in thereaction in Table 1.

Epoxide 3e. The general procedure was followed using boronate ester 2e(80 mg, 0.25 mmol) and mCPBA (106 mg, 0.475 mmol), giving the product asa white solid (51 mg, 64%). d.r.>20:1. X-ray quality crystals wereobtained by making a saturated solution of 3e in 1 mL of1,2-dichloroethane and layering it with about 2 mL of hexane. The layerswere allowed to slowly mix at room temperature, giving the desiredcrystals. TLC (Hexanes:acetone 3:2) R_(f)=0.46, visualized by KMnO₄; ¹HNMR (500 MHz, CD₃CN) δ 4.29 (dt, J=10.5, 6.5 Hz, 1H), 4.20 (d, J=17 Hz,1H), 3.98 (d, J=15 Hz, 1H), 3.65 (d, J=15 Hz, 1H), 3.42 (d, J=17 Hz,1H), 3.07 (m, 1H), 2.72-2.66 (m, 1H), 2.51-2.45 (m, 1H), 2.17-2.14 (m,1H), 2.12 (d, J=3 Hz, 1H), 2.05 (sept, J=3 Hz, 1H), 1.94 (dt, J=6, 2.5Hz, 1H), 1.81 (ddd, J=15, 6. 2.5 Hz, 1H), 1.37 (d, J=5 Hz, 3H), 1.33 (d,J=7 Hz, 3H), 1.27 (s, 3H), 1.04 (s, 3H), 0.92 (d, J=10 Hz, 1H); ¹³C NMR(125 MHz, CDCl₃) δ 169.2, 166.3, 109.7, 67.9, 61.7, 54.6, 53.2, 49.0,40.6, 39.2, 38.9, 32.1, 30.5, 27.0, 23.6, 23.5; ¹¹B-NMR (128 MHz, CDCl₃)δ 10.7; HRMS (ESI+) Calculated for C₁₇H₂₇BNO₅: 336.1982, Found:336.1977.

Epoxide 3f. The general procedure was followed using boronate ester 2f(84 mg, 0.25 mmol) and mCPBA (106 mg, 0.475 mmol), giving the product asa white solid (68 mg, 77%). d.r.>20:1. TLC (Hexanes:acetone 3:2)R_(f)=0.22, visualized by KMnO₄; ¹H NMR (500 MHz, acetone-d₆) δ 4.29 (d,J=18 Hz, 1H), 4.30-4.26 (m, 1H), 4.13 (d, J=15.5 Hz, 1H), 4.06 (d,J=18.5 Hz, 1H), 3.98 (d, J=15.5 Hz, 1H), 3.02 (dt, J=6, 3 Hz, 1H),2.80-2.74 (m, 1H), 2.57-2.51 (m, 1H), 2.50-2.44 (m, 1H), 1.97 (dt, J=6,2.5 Hz, 1H), 1.79 (ddd, J=15, 6. 2.5 Hz, 1H), 1.39 (d, J=7.5 Hz, 3H),1.28 (s, 3H), 1.10 (d, J=10.5 Hz, 1H), 1.05 (s, 3H); ¹³C NMR (125 MHz,acetone-d₆) δ 170.7, 167.2, 68.8, 64.1, 61.9, 57.8, 55.4, 50.2, 41.6,39.7, 39.1, 32.3, 31.2, 27.4, 23.9, 23.7; ¹¹B-NMR (128 MHz, acetone-d₆)δ 10.8; HRMS (ESI+) Calculated for C₁₇H₂₇BNO₆: 352.1931, Found:352.1925.

Epoxide 3 g. The general procedure was followed using boronate ester 2 g(45 mg, 0.1 mmol) and mCPBA (106 mg, 0.475 mmol), giving the product asa white solid (35 mg, 75%). d.r.>20:1. TLC (Hexanes:acetone 3:2)R_(f)=0.51, visualized by KMnO₄; ¹H NMR (500 MHz, CDCl₃) δ 4.31 (dt,J=10.5, 6 Hz, 1H), 4.21 (d, J=18 Hz, 1H), 4.01 (dd, J=12.5, 2.5 Hz, 1H),3.99 (d, J=15.5 Hz, 1H), 3.64 (d, J=15 Hz, 1H), 3.63 (dd, J=12.5, 4.5Hz, 1H), 3.42 (d, J=17 Hz, 1H), 3.17 (quint, J=3 Hz, 1H), 2.70-2.65 (m,1H), 2.50-2.46 (m, 1H), 2.39 (d, J=3 Hz, 1H), 2.16-2.15 (m, 1H), 2.05(sept, J=3 Hz, 1H), 1.95 (dt, J=6.5, 2.5 Hz, 1H), 1.81 (ddd, J=15, 6, 3Hz, 1H), 1.33 (d, J=6.5 Hz, 3H), 1.27 (s, 3H), 1.02 (s, 3H), 0.89 (s,9H), 0.07 (s, 3H), 0.07 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ 169.2,166.3, 67.9, 63.2, 61.7, 57.2, 54.6, 49.0, 40.6, 39.2, 38.9, 32.0, 30.5,27.0, 25.9, 23.5, 23.5, 18.3, −5.3, −5.4; ¹¹B-NMR (128 MHz, CDCl₃) δ11.3; HRMS (ESI+) Calculated for C₂₃H₄₁BNO₆Si: 466.2796, Found:466.2798.

Epoxide 3 h. The general procedure was followed using boronate ester 2 h(76 mg, 0.25 mmol) and mCPBA (106 mg, 0.475 mmol), giving the product asa white solid (66 mg, 82%). d.r.>20:1. X-ray quality crystals wereobtained by making a saturated solution of 3 h in 1 mL of1,2-dichloroethane and layering it with about 2 mL of hexane. The layerswere allowed to slowly mix at room temperature, giving the desiredcrystals. TLC (Hexanes:acetone 3:2) R_(f)=0.43, visualized by KMnO₄; ¹HNMR (500 MHz, CDCl₃) δ 4.29 (dt, J 10.5, 6.5 Hz, 1H), 4.22 (d, J 17.5Hz, 1H), 3.98 (d, J 15 Hz, 1H), 3.68 (d, J 15 Hz, 1H), 3.48 (d, J 17 Hz,1H), 2.87 (dd, J 6, 5 Hz, 1H), 2.78 (dd, J 6, 3.5 Hz, 1H), 2.72-2.66 (m,1H), 2.51-2.45 (m, 1H), 2.39 (dd, J=5, 3.5 Hz, 1H), 2.18-2.17 (m, 1H),2.06 (sept, J 3 Hz, 1H), 1.95 (dt, J 6, 2 Hz, 1H), 1.83 (ddd, J 15, 6.2.5 Hz, 1H), 1.34 (d, J 7 Hz, 3H), 1.27 (s, 3H), 1.03 (s, 3H), 0.92 (d,J 11 Hz, 1H); ¹³C NMR (125 MHz, CDCl₃) δ 169.5, 166.6, 68.1, 61.6, 54.7,49.0, 45.5, 40.6, 39.2, 38.9, 32.0, 30.5, 27.0, 23.5, 23.5; ¹¹B-NMR (128MHz, CDCl₃) δ 11.0; HRMS (ESI+) Calculated for C₁₆H₂₅BNO₅: 322.1826,Found: 322.1824.

Example 10 Pinacol-Type Rearrangement of Epoxide 3a

Preliminary studies have also revealed that oxiranyl PIDA boronates canbe transformed into previously inaccessible Csp³ boronate buildingblocks. For example, Mg(ClO₄)₂ promotes a very interesting pinacol-typerearrangement¹² (House et al. (1955) J Am Chem Soc 77:3070-5; Parker etal. (1959) Chem Rev 59:737; Rickborn in Comprehensive Organic Synthesis,Trost, Ed., Pergamon: Oxford, 1991, Vol. 3, Chapter 3.3, pp 733-75) of3a to generate air stable α-boryl aldehyde 4 (Scheme 1 in FIG. 2).Stable α-boryl aldehydes do not appear to have been previously reportedin the literature, and the stability of 4 is likely attributable to theunique properties of the iminodiacetic acid boronate motif. Importantly,this rearrangement also occurs with complete maintenance ofstereochemical purity.

A dry Schlenk flask was charged with 3a (795 mg, 2 mmol) and dry CH₂Cl₂(40 mL) under a nitrogen atmosphere. The flask was flushed with nitrogenand cooled to 0° C. Mg(ClO₄)₂ (2 mmol) was then added in one portion,and the reaction was stirred in the ice/water bath for 2 h. The reactionwas then warmed up to room temperature and filtered through Celite,washing with additional CH₂Cl₂ (20 mL). (Any residual Mg(ClO₄)₂ may beremoved by pushing the filtrate through a solvent-resistant syringefilter. PTFE filters from Sigma-Aldrich (product #54132-U) were used).The filtrate was then concentrated in vacuo at room temperature toafford an off-white solid (667 mg, 84%, d.r.>20:1 by 1H NMR based onaldehyde resonances). No purification of this product was necessary forsubsequent reactions. Note: the stereogenic α-carbon of the aldehyde canepimerize on silica gel.

Results. ¹H NMR (500 MHz, acetone-d₆) δ 9.88 (d, J=2.5 Hz, 1H), 7.45(dd, J=7, 1.5 Hz, 2H), 7.39 (t, J=7.5 Hz, 2H), 7.32 (tt, J=7.5, 1.5 Hz,1H), 4.29 (d, J=18 Hz, 1H), 4.07 (d, J=18 Hz, 1H), 4.04 (d, J=15.5 Hz,1H), 3.93 (br s, 1H), 3.66 (d, J=10.5, 6 Hz, 1H), 2.98-2.92 (m, 1H),2.86 (d, J=15.5 Hz, 1H), 2.45 (ddt, J=11, 6, 2 Hz, 1H), 2.38 (ddt, J=13,6.5, 2 Hz, 1H), 2.11 (sept, J=3 Hz, 1H), 1.88-1.86 (m, 1H), 1.85-1.83(m, 1H), 1.26 (s, 3H), 1.08 (d, J=11 Hz, 1H), 0.99 (s, 3H), 0.93 (d, J=7Hz, 3H); ¹³C NMR (125 MHz, CDCl₃) δ 199.9, 168.5, 166.1, 134.4, 129.4,128.7, 127.4, 67.0, 61.6, 55.3, 48.8, 40.6, 38.8, 38.6, 31.6, 30.3,27.0, 23.1, 23.0; HRMS (ESI+) Calculated for C₂₂H₂₉BNO₅: 398.2139,Found: 398.2140.

Example 11 Reduction of Stable α-Boryl Aldehyde 4 to Alcohol 5

Stable α-boryl aldehydes such as 4 represent a new type ofnucleophilic/electrophilic bifunctional reagent. The substantialpotential of this motif for further structural modification has begun tobe explored. For example, 4 can be readily reduced to alcohol 5 (thisExample) or ketalized to generate complex Csp³ boronate 6 (see Example12).

A dry 20 mL Schlenk flask was charged with aldehyde 4 (397 mg, 1 mmol)under an atmosphere of nitrogen. CH₂Cl₂ (20 mL) was added and thesolution was cooled to −20° C. NaBH(OAc)₃ (318 mg, 2 mmol) was addedportionwise to the solution over 5 min. Following the addition, AcOH (4mL) was added, and the reaction was allowed to stir at −20° C. for 3 h.After warming to 0° C., the reaction was quenched by the addition ofsat. aqueous NaHCO₃ solution (10 mL). The mixture was stirred for 10min, then transferred to a separatory funnel. After phase separation,the organic layer was washed twice with sat. aqueous NaHCO₃ solution (10mL), then with H₂O (10 mL) and dried over MgSO₄, filtered andconcentrated. The solid residue was washed with Et₂₀, then filtered anddried in vacuo. A white solid was obtained (287 mg, 72%).

Results. TLC (Hexanes:acetone) R_(f)=0.32, visualized by KMnO₄; ¹H NMR(500 MHz, acetone-d₆) δ 7.39 (app d, J=7.5 Hz, 2H), 7.33 (app t, J=7.5Hz, 2H), 7.24 (app t, J=7 Hz, 1H), 4.29 (d, J=18 Hz, 1H), 4.07 (d, J=18Hz, 1H), 4.04 (d, J=15.5 Hz, 1H), 3.66 (d, J=10.5, 6 Hz, 1H), 2.82 (d,J=15 Hz, 1H), 2.82-2.77 (m, 1H), 2.61 (dd, J=6, 4 Hz, 1H), 2.44 (ddt,J=11, 6, 2 Hz, 1H), 2.33 (ddt, J=13, 6.5, 2 Hz, 1H), 2.08 (m, 2H), 1.86(dt, J=5.5, 2 Hz, 1H), 1.76 (ddd, J=14.5, 6, 2.5 Hz, 1H), 1.27 (s, 3H),1.05 (d, J=11 Hz, 1H), 1.01 (s, 3H), 0.93 (d, J=7 Hz, 3H); HRMS (ESI+)Calculated for C₂₂H₃₁BNO₅: 400.2295, Found: 400.2297.

Example 12 Ketalization of Stable α-Boryl Aldehyde 4 to Acetal 6

A 40 mL Ichem vial equipped with a stir bar was charged with aldehyde 4(397 mg, 1 mmol), (S,S)-hydrobenzoin (643 mg, 3 mmol) and MgSO₄ (1 g).CH₂Cl₂ (20 mL) was added, followed by pTsOH.H₂O (3.8 mg, 0.02 mmol). Thevial was flushed briefly with nitrogen and placed in a heat block. Thereaction was stirred at 35° C. for 3 h. After cooling to roomtemperature, the suspension was filtered through Celite® and thefiltrate was concentrated in vacuo. The crude product was purified bysilica gel chromatography (acetone/Et₂O/hexane 1:4:15→1:2:7→1:1:3) toafford 6 (394 mg, 66%) as a white solid. X-ray quality crystals wereobtained by layering a solution of 6 in 1 mL of 1,2-dichloroethane andlayering it with about 2 mL of hexane. The layers were allowed to slowlymix at room temperature, giving the desired crystals.

Results. TLC (Hexanes:EtOAc:Et₂O 2:2:1) R_(f)=0.69, visualized by shortwave UV; ¹H NMR (500 MHz, CDCl₃) δ 7.61, (app d, J=6.5 Hz, 2H), 7.38(app t, J=7.5 Hz, 2H), 7.32-7.25 (m, 7H), 7.19-7.17 (m, 2H), 7.15-7.13(m, 2H), 6.04 (d, J=2.5 Hz, 1H), 4.75 (d, J=8 Hz, 1H), 4.31 (d, J=8 Hz,1H), 4.17 (d, J=17.5 Hz, 1H), 3.79 (dt, J=10, 6 Hz, 1H), 3.44 (d, J=15Hz, 1H), 3.42 (d, J=17 Hz, 1H), 3.00 (d J=2.5 Hz, 1H), 2.92 (d, J=15 Hz,1H), 2.77-2.72 (m, 1H), 2.44-2.42 (m, 1H), 2.07 (m, 1H), 1.96 (m, 1H),1.85-1.81 (m, 2H), 1.26 (s, 3H), 0.96 (s, 3H), 0.91-0.89 (m, 4H); ¹³CNMR (125 MHz, CDCl₃) δ 168.9, 166.5, 138.7, 137.7, 136.5, 130.8, 128.6,128.4, 128.3, 128.2, 127.9, 127.2, 126.9, 126.4, 106.1, 87.4, 84.9,66.4, 61.6, 55.3, 48.8, 40.6, 38.9, 38.8, 31.7, 30.9, 30.3, 27.0, 23.2,23.1; HRMS (ESI+) Calculated for C₃₆H₄₁BNO₆: 594.3027, Found: 594.3028.

Example 13 1,2-Boryl Migration

Single crystal X-ray analysis of 6 enabled the full stereochemicalassignment of 4, which is consistent with exclusive migration of theboronate group during the rearrangement of 3a. This type of 1,2-borylmigration appears never to have been previously reported in theliterature. This finding further suggests that the potential of thisplatform to access a unique array of novel Csp³ boronate building blocksis substantial.

Example 14 Epoxidation of Alkenyl Boronates

Table 3 summarizes the general scheme and results of a number ofreactions for epoxidation of alkenyl boronates that have been performedusing stereoisomerically enriched or substantially pure chiralorganoboronic acids of the invention.

TABLE 3 Epoxidation of alkenyl boronates.

Entry 1 2 d.r.^(a) 1

 2.1:1  2

 2.7:1  3

   4:1  4

 1.6:1  5

>20:1 6

>20:1 7

 12:1 8

~20:1  9

>20:1 10

>20:1 11

>20:1 12

>20:1 13

  5:1 ^(a)d.r. = diastereomeric ratio as determined via 500 MHz ¹H NMRanalysis of unpurified reaction mixtures.

Example 15 General Apparatus Design Principles

One example of an automated small molecule synthesizer is shown in FIG.4 (photograph) and FIG. 5 (schematic). This custom-designed apparatuscan execute the fully automated synthesis of eight small moleculessimultaneously. Each synthesis consists of between one and threeiterative coupling sequences, where each coupling sequence can include adeprotection step, a cross-coupling step and a purification step. Theorganization of the apparatus is centered on eight main syringe pumps.Each main syringe pump is dedicated to only one synthesis. These eightmain syringe pumps operate independently to execute iterative couplingsequences in parallel. Resources for each synthesis arecompartmentalized such that each main syringe pump does not access theresources of another main syringe pump, with the following exceptions:all solvents and all product output ports are shared by all of the mainsyringe pumps. Additionally, an auxiliary syringe pump is used as ashared resource for the purification steps. Another auxiliary syringepump is used as a shared resource to handle all aqueous solutions. Thecustom designed software that operates the machine governs how theshared resources are distributed.

Standard Valve. The valve modules were purchased from J-KEM Scientific(part #Syr-CS4) and are connected to the controlling computer via aRS485 to USB connection. Each valve module is equipped with foureight-port stream-selecting valves (J-KEM, part #SPDV-CS8). Each valveconnects the input stream, which enters through the center of the valve,to one of eight possible output streams (ports A thru H). The locationof the standard valves is shown in FIG. 5.

Syringe Pump Valve. Each syringe pump is fitted with an eight-portstream selecting valve (J-KEM, part #SPDV8) where the input streamenters from the syringe connected immediately in front of port “E”. Port“E” is partially blocked by the syringe and requires a flush-net fitting(IDEX Health and Science, part #F-358) to connect the output stream. Thelocation of the syringe pump valves is shown in FIG. 5.

Syringe Pumps. Syringe pumps were purchased from J-KEM Scientific (part#SYR1400-8 for P1-P8, part #SYR-1400PC for P9 and P10) and are connectedto the controlling computer via a RS485 to USB connection. Each syringepump is fitted with an eight-port stream-selecting valve (J-KEM, part#SPDV8) and a 10 mL glass syringe equipped with a Teflon plunger (J-KEM,part #SPGS-10000). The syringe pump withdraws and injects at rates from0.0 mL/min to 70.0 mL/min with a step of 0.0029 mL. The location of thesyringe pumps is shown in FIG. 5.

Reaction Tubes. To minimize cross-contamination and allow the rapidsetup of a synthesis, all chemical manipulations are performed indisposable polypropylene tubes purchased from Luknova, item #FC003012.The dimensions of the tube are 21 mm×120 mm (ID×length). The bottom ofthe tube is fitted with a 21 mm diameter×5 mm tall frit. The bottom ofthe tube is accessed through a male Luer tip, while the top of the tubeis sealed with an air-tight, threaded cap containing a female Luer port.The tube holds a solvent volume of up to 25 mL. Examples of reactiontubes are shown in FIG. 6 and FIG. 8.

Tubing and Fittings. All tubing and fittings were purchased from IDEXHealth and Science. The tubing used in the machine is 0.030 inch (ID)×1/16 inch (OD) Teflon FEP tubing (part #1520xL). All tubing connectionswere made with 1/16 inch ETFE flangeless ferrules (part #P-200x) and¼-28 acetal fittings (part #P-202x). Male Luer fittings (part #P-625)and female Luer fittings (part #P-658) are ETFE and PEEK, respectively.Examples of tubes and fittings are shown in FIG. 6.

Example 16 Computer Control of Apparatus

General Programming Design Principals. All apparatus equipment iscontrolled by a custom program written in VB.NET using Microsoft VisualBasic 2008 Express Edition. The apparatus is controlled by a singlecomputer running Windows Vista. The apparatus is designed to run anexperiment independently on each of the eight main syringe pumps. Eachmain pump can be started and stopped at will without affecting the otherpumps. Further, the scripts of simultaneously executing experiments donot need to be the same nor do they need to be synchronized in order forthe experiments to perform successfully. The program is designed tomanage distribution of shared resources such as common valve equipmentand auxiliary syringe pumps as well as bandwidth on the COM ports.

Setting up and modifying the script used to execute an experiment isdesigned to be straightforward and facile. Towards this end, a simplecustom scripting language was developed. The scripting language containsa small collection of commands used to send instructions to a virtualmachine, manage the timing of these operations, and lock/unlock accessto shared resources. The program serves as an interpreter for thiscustom scripting language and maps the virtual machine instructions tothe required apparatus hardware. In this way the same script can be usedon any of the main syringe pumps without modification.

Communication to the Apparatus Equipment. Commands are sent to theapparatus equipment using the computer's serial ports. The RS485 serialports of the apparatus equipment are connected to a serial-to-USBconverter which is connected to the computer. Each COM port can addressup to 16 pieces of equipment, where a piece of equipment is defined as avalve or a syringe pump. The syringe pump may or may not additionallycontrol a solenoid valve. As configured, communication to the apparatusis distributed across four COM ports. Commands can be sent to theequipment no faster than every 20 milliseconds. To enforce this delay,the program maintains a queue of commands to be sent to the equipment.Commands recognized by the equipment are: move the valve to a specificport, report the current position of the valve, move the syringe plungerto a specific position at a specific rate, turn the solenoid valveon/off, and report if the equipment has finished executing the previouscommand.

Program Architecture. Each valve and each syringe pump is representedprogrammatically as an “equipment object”. Each of these equipmentobjects is given an identifier that can be used to map the commands ofthe scripting language to the actual hardware represented by theequipment object. Each main pump is assigned a “pump object” that is acontainer for all of the equipment objects that represent resources thatare available to the main pump. No single pump object contains everyequipment object, but every equipment object is contained in at leastone pump object. When an experiment is executed on the main pump, thelist of scripted commands is passed as a text file to the correspondingpump object. The pump object is responsible for proof-reading,interpreting and executing the scripted commands and updating thegraphic user interface (GUI) as appropriate.

Script Execution. When the pump object is passed a text file of commandlines, the pump object interprets each command line into a “commandobject”. The command object contains all of the information that isnecessary to execute the command. Once a command object is created it isentered into a queue managed by the pump object. Through this processthe script is proof-read to identify any syntax errors that wouldprevent the code from executing properly. The script is then executingby retrieving an item from the queue, sending the appropriate commandsto the equipment via the COM port, periodically checking the status ofthe machine equipment until the command is complete, and then repeatingthe process for the next command in the queue.

Scripting Language. The scripting language contains the followingcommands with indications on their usage:

' (apostrophe) Indicates everything following the apostrophe is acomment and should not be interpreted. [text] (brackets) The bracketsrepresent a placeholder value recognized by the identifier text thatwill be replaced at runtime with the define command. define text = valueAt runtime replaces all brackets (placeholders) containing text with thevalue of value. This is a useful strategy for writing flexible scripts.pause n Halts execution of the script for n seconds. valve nL Movesvalve n to port position L (A-H). valve xon valve xon opens the solenoidvalve associated with the valve xoff main syringe pump. valve xoffcloses this solenoid valve. pump n in = L out = M Fills the syringe withn mL drawn from port position L ratein = x rateout = y (A-H) at a rateof x mL/min. and inject n mL out through port position M (A-H) at ymL/min. The port position refers to the valve that is directly connectedto the syringe. Omitting the in = portion instructs the pump to onlydispense n mL as per above. Omitting the out = portion instructs thepump to only fill n mL as per above. Use rate = x to set both the rateof withdrawal and the rate of injection to x mL/min. pump out = M rate =x Injects the entire contents of the syringe out through port position M(A-H) at a rate of x mL/min. log “comment text” Writes a time-stampedentry to the log book containing the user-defined text (comment text).lock n Claims valve n for the exclusive use by the main pump. If valve nis busy or has been locked by a different pump, execution of the scriptis halted until the valve becomes available. Auxiliary pumps can also belocked using this command. unlock n Releases valve n from the exclusiveuse by the main pump. All lock commands should be eventually followed byan unlock command. Auxiliary pumps can also be released using thiscommand. sub sub_name The sub and end sub commands mark the beginningand end sub end, respectively, of command lines that will be interpretedas a sub routine with the identifier sub_name. run sub_name Runs the subroutine identified as sub_name. This sub routine should have beenpreviously defined using the sub and end sub commands. The commandfollowing the run command is not executed until all of the commands inthe sub routine have completed (as opposed to the background command.)background sub_name Runs the sub routine identified as sub_name. Thiscommand is similar to the run command except that as soon as the subroutine begins to execute, the command following the background commandexecutes as well. Therefore, the sub routine is handled as a backgroundprocess allowing multiple actions to be performed at once. wait sub_nameHalts execution of the script until the sub routine identified assub_name (which was previously executed using the background command)finishes its execution. This command allows background processes to besynchronized with the main script.

Example 17 Chemical Synthesis

The following example, while not specific to a PIDA-based system,describes procedures that, when used with a PIDA-based system, arereasonably expected to achieve similarly effective results.

General Procedure. All chemical manipulations were performed inpolypropylene tubes purchased from Luknova, item #FC003012. Thedimensions of the tube are 21 mm×120 mm (ID×length). The bottom of thetube is fitted with a 21 mm diameter×5 mm tall frit. The bottom of thetube is accessed through a male Luer tip, while the top of the tube issealed with an air-tight, threaded cap containing a female Luer port.The tube holds a solvent volume of up to 25 mL.

Deprotection Tubes. To enable automation, a novel MIDA boronatedeprotection method was developed using Amberlyst A26(OH) resin.Amberlyst A26(OH) was purchased from Sigma-Aldrich and was stored underN₂ atm. at 4° C. Amberlyst A26(OH) (suspension volume of 20 mL) wastwice washed with MeCN (50 mL) with vigorous agitation for 60 seconds ineach wash. The residual solvent was evaporated under a fast stream ofair for 5 minutes until the resin was light beige in color and wasfree-flowing. To each polypropylene tube was added the Amberlyst resin(2.0 g resin for every 1.0 mmol of MIDA boronate to be deprotected) and,optionally, the MIDA boronate starting material. The tube was capped andthen placed on the machine where the bottom Luer tip connected to thedeprotection table and the top Luer port is covered with aluminum foil.

Drying and Degassing Tubes. A polypropylene tube was charged withCelite®, activated molecular sieves (4 Å, 8-12 mesh) and K₂CO₃. Theamounts of these reagents are proportional to the amount of AmberlystA26 resin used in the deprotection step prior to drying/degassing, asindicated below. Onto the bed of solids was placed a plastic plunger,cut from the plunger of a 5 mL polypropylene syringe (Fisher #14-817-28,Norm-Ject). The plunger prevents the solids from lifting during thedegassing step. The tube was capped and then placed on the machine wherethe bottom Luer tip connects to the degassing table and the top Luerport is connected to the gas manifold.

Amberlyst A26 (previous step) Celite ® Mol. sieves K₂CO₃ 2.0 g 200 mg2.0 g 2.0 g 1.0 g 100 mg 1.0 g 1.0 g 0.5 g  50 mg 0.5 g 0.5 g

Reaction Tubes. To assist in the transfer of small amounts of Pd(OAc)₂and S-Phos, these reagents were adsorbed onto Cs₂CO₃ as follows. To a 40mL glass vial was added Pd(OAc)₂ (22 mg) and Cs₂CO₃ (2.723 g). To thevial was added THF (10 mL), and the suspension was concentrated in vacuoto afford a pale amber powder, the Pd-mixture. To a 40 mL glass vial wasadded S-Phos (76 mg) and Cs₂CO₃ (2.667 g). To the vial was added THF (10mL), and the suspension was concentrated in vacuo to afford a whitepowder, the SPhos-mixture.

To a polypropylene tube was added a stir bar (Big Science Inc.,SBM-1508-REH), the halide (0.333 mmol), the Pd-mixture (488 mg, 5% Pd)and the SPhos-mixture (488 mg, 10% S-Phos). For aqueous couplings, tothe tube was added a KOH pellet (75 mg, 1.7 mmol). The tube was cappedwith a modified cap (see detail) and was placed in a heating block. Thebottom of the tube is connected the reaction table, the top of the tubeis vented to the gas manifold, and the second top input is connected tothe reaction table for addition of the boronic acid. Building on thepreviously published reports of “slow-release” cross-coupling, theboronic acid was added slowly via syringe pump to minimize in situdecomposition and thereby maximize yields.

Automation. Each cross-coupling in the automated sequence was performedaccording to the following, fully automated script:

-   -   Deprotection a) Add THF (5 mL) to deprotection tube.    -   b) Agitate the mixture via gas bubbling for 60 minutes.    -   c) Add AcOH in THF (4.0 M, 5.0 mmol per 1.0 g of Amberlyst        resin).    -   d) Agitate the mixture via gas bubbling for 15 minutes.    -   e) Transfer the solution to the drying tube, washing the resin        with THF (5×1.0 mL).    -   f) Sparge the mixture with Ar gas for 15 minutes.    -   g) While sparging the reaction tube with Ar gas for 15 min.,        agitate the THF mixture via gas bubbling every 2 minutes.    -   Cross-Coupling h) Add THF (3 mL) to the reaction tube and allow        the mixture to stir for 10 min.    -   i) Transfer the boronic acid solution from the drying tube to        the reaction tube over 120 min., washing the solids with THF        (3×1.0 mL).    -   j) Stir the reaction mixture at 150 rpm for 22 hours.    -   Purification k) Add hexanes (12 mL) to the ppt. chamber, then        add a portion of the reaction solution (3 mL) to the ppt.        chamber.    -   l) Withdraw the solution in the ppt. chamber through the SiO₂        plug and send to waste.    -   m) Repeat steps (k) and (l) until all of the reaction solution        has been transferred.    -   n) Add Et₂O w/MeOH (1.5% v/v) (7.5 mL) to the ppt. chamber,        withdraw the solution through the SiO₂ plug, and send to waste.        Repeat an additional four times.    -   o) Add Et₂O (7.5 mL) to the ppt. chamber, withdraw the solution        through the SiO₂ plug, and send to waste. Repeat an additional        two times.    -   p) Flow Ar gas through the SiO₂ plug for three minutes to        evaporate residual solvent.    -   q) Add THF (6.8 mL) to the ppt. chamber.    -   r) Withdraw the THF solution through the SiO₂ plug and then        inject the solution back into the ppt. chamber. Repeat an        additional two times.    -   s) Withdraw the THF solution through the SiO₂ plug and inject        the solution into the deprotection tube used in the next        reaction. The next reaction begins at step a.

Direct release/aqueous coupling modification (typically performed as thelast step of an automated synthesis). This sequence begins after step(s) from the general automation script (above).

-   -   t) Sparge the THF solution derived from the purification of the        previous cross-coupling with Ar gas for 15 minutes.    -   u) Transfer the THF solution to the reaction tube in one        portion.    -   v) Stir the mixture for 5 minutes.    -   w) Add degassed H₂O (2 mL) to the reaction tube.    -   x) Stir the reaction mixture at room temperature for 12 hours.    -   y) Add aq. NH₄Cl (2.5 mL), mix for 5 minutes, then withdraw the        entirety of the mixture and transfer it to the product test        tube.

β-parinaric acid. All steps were performed according to the generalprocedure. The machine was equipped with reagent tubes as follows.

Step 1. The machine was equipped with a deprotection tube charged withAmberlyst resin (2.0 g) and MIDA boronate 1 (211 mg, 1.0 mmol); a dryingtube charged with molecular sieves (2.0 g), K₂CO₃ (2.0 g) and Celite®(0.2 g); and a reaction tube charged with the Pd-mixture (488 mg), theSPhos-mixture (488 mg) and boronate 2 (103 mg, 0.333 mmol).

Step 2. The machine was equipped with a deprotection tube charged withAmberlyst resin (1.0 g); a drying tube charged with molecular sieves(1.0 g), K₂CO₃ (1.0 g) and Celite® (0.1 g); and a reaction tube chargedwith the Pd-mixture (244 mg), the SPhos-mixture (244 mg), and boronate 2(34 mg, 0.11 mmol).

Step 3. The machine was equipped with a deprotection tube (empty, butused for sparging the MIDA boronate solution) and a reaction tubecharged with the Pd-mixture (60 mg), the SPhos-mixture (60 mg), KOH (75mg, 1.7 mmol) and halide 3 (11 mg, 0.037 mmol).

Automation. The synthesis was performed in a fully automated fashionwith no operator intervention. Step 1 and step 2 were performedfollowing the standard script, and step 3 was performed following thedirect release/aqueous coupling modification of the standard script. Theaqueous mixture that was outputted from the machine was manuallypurified as follows: The mixture was transferred to a 60 mL separatoryfunnel and was diluted with sat. aq. NH₄Cl (10 mL). The mixture wasextracted twice with Et₂O (20 mL) and the combined organics were washedwith brine (20 mL); dried over MgSO₄; filtered, then concentrated invacuo. The yellow residue was purified via Sift chromatography to affordβ-parinaric acid as a white solid (yield not yet determined). The ¹H NMR(CDCl₃) spectrum of the synthesized product was fully consistent withthe literature data (Lee, S. J.; Gray, K. C.; Paek, J. S.; Burke, M. D.J. Am. Chem. Soc., 2008, 130, 466-468).

To characterize the efficiency of each step and characterize allintermediates, Step 1 was repeated and the MIDA boronate solutiongenerated in line 19 of the standard script was diverted into a testtube and then concentrated to afford pure intermediate 4 as a colorlesssolid (40 mg, 52%).

¹H NMR (500 MHz, acetone-d₆): δ 6.53 (dd, J=17.0, 10 Hz, 1H), 6.11 (dd,J=15.5, 10.0 Hz, 1H), 5.82 (dt, J=15.5, 6.5 Hz, 1H), 5.54 (d, J=17.5 Hz,1H), 4.20 (d, J=17.0 Hz, 2H), 4.01 (d, J=17.0 Hz, 2H), 2.98 (s, 3H),2.10 (quint, J=7.5 Hz, 2H), 0.99 (t, J=7.5 Hz, 3H); ¹³C NMR (125 MHz,acetone-d₆): δ 196.1, 143.7, 137.8, 132.6, 62.2, 47.2, 26.1, 13.7.

Step 1 and step 2 were repeated and the MIDA boronate solution generatedduring the second coupling (line 19 of the standard script) was divertedinto a test tube and then concentrated to afford pure intermediate 5 asa colorless solid (22 mg, 76%).

¹H NMR (500 MHz, acetone-d₆): δ 6.58 (dd, J=18.0, 10.5 Hz, 1H), 6.28(dd, J=15.0, 10.0 Hz, 1H), 6.20 (dd, J=15.0, 10.0 Hz, 1H), 6.11 (ddt,J=15.5, 10.5, 1.5 Hz, 1H), 5.82 (dt, J=15.0, 6.5 Hz, 1H), 5.64 (d,J=17.5 Hz, 1H), 4.21 (d, J=17.0 Hz, 2H), 4.03 (d, J=17.0 Hz, 2H), 2.99(s, 3H), 2.12 (quint, J=7.5 Hz, 2H), 0.99 (t, J=7.5 Hz, 3H); ¹³C NMR(125 MHz, acetone-d₆): δ 169.0, 143.5, 138.3, 134.8, 133.5, 130.3, 62.2,47.3, 26.4, 13.8.

all-trans-retinal. All steps were performed according to the generalprocedure. The machine was equipped with reagent tubes as follows.

Step 1. The machine was equipped with a deprotection tube charged withAmberlyst resin (1.0 g) and MIDA boronate 6 (173 mg, 0.500 mmol); adrying tube charged with molecular sieves (1.0 g), K₂CO₃ (1.0 g) andCelite® (0.1 g); and a reaction tube charged with the Pd-mixture (244mg), the SPhos-mixture (244 mg) and boronate 2 (52 mg, 0.111 mmol).

Step 2. The machine was equipped with a deprotection tube charged withAmberlyst resin (0.5 g); a drying tube charged with molecular sieves(0.5 g), K₂CO₃ (0.5 g) and Celite® (50 mg); and a reaction tube chargedwith the Pd-mixture (82 mg), the SPhos-mixture (82 mg). A separatepolypropylene tube was charged with a solution of halide 7 (0.056 mmol)in degassed THF (3 mL).

Automation. The synthesis was performed in a fully automated fashionwith no operator intervention. Step 1 was performed following thestandard script. Step 2 was performed following the standard directrelease/aqueous coupling modification script with the additionalmodification that the THF used in line 8 of the standard script was theentirety of the solution containing halide 7. Further, the script forstep 2 was stopped after line 10 and the reaction solution was outputtedto a test tube. The product was manually purified as follows: Thereaction solution was concentrated in vacuo and the solid yellow residuewas purified by SiO₂ chromatography using an Isco-Teledyne CombiFlashsystem to afford all-trans-retinal as a yellow solid (3.3 mg, 20%). The¹H NMR (CDCl₃) spectrum of the product was fully consistent with theliterature data (Lee, S. J.; Gray, K. C.; Paek, J. S.; Burke, M. D. J.Am. Chem. Soc., 2008, 130, 466-468).

Example 18 Generality of Purification Platform

The following example, while not specific to a PIDA-based system,describes procedures that, when used with a PIDA-based system, arereasonably expected to achieve similarly effective results.

To establish the generality of the novel purification platform, itscapacity to purify a series of MIDA boronates representing a diverserange of structures, including aryl, heteroaryl, alkynyl, alkenyl, andalkyl derivatives, was tested. Briefly, mock crude reaction mixtureswere prepared by mixing each MIDA boronate (1 equiv.) (Table 4) withtolyl-boronic acid (1 equiv.) and a palladium catalyst (0.1 equiv) inTHF. Each of these mixtures was then subjected to fully-automatedpurification via the hybrid precipitation/catch-and-release platformdescribed in detail herein. At the end of this process, all of theseMIDA boronates were obtained in >90% purity as judged by ¹H NMR, and theyields of recovered MIDA boronates were good to outstanding (Table 4).

TABLE 4 Purification from mock crude reaction mixtures.

Boronate % Recovery

69

76

53

86

92

87

92

90

92

68

83

94

81

86

78

65

Details of the procedure are as follows.

Pre-activation of the Catalyst Solution: Palladium(II) acetate (0.001875mmol, 2.5 mol %) and SPhos (0.00375 mmol, 5 mol %) per purification tobe run were combined in an 8 mL scintillation vial equipped with aPTFE-coated magnetic stir bar and placed under an argon atmosphere. THFwas added to generate a 0.01 M catalyst stock solution (with respect topalladium(II) acetate), and it was stirred vigorously for 30 min at roomtemperature to generate an orange, yellow, or clear solution. After thisactivation process, 1 mL catalyst stock solution was added to thesolution in the polypropylene cartridge containing the simulatedreaction mixture.

Preparation and Installation of Simulated Reaction Chamber: A new fitted12 g Luknova polypropylene cartridge was charged with MIDA boronate(0.075 mmol, 1 eq), 4-methylbenzene boronic acid (0.075 mmol, 1 eq), andTHF (10 mL). After addition of the pre-activated catalyst solution, thecartridge was installed into the Luer fittings in the reaction block ofthe automated synthesizer. Once all cartridges were in place, theautomated purification routine was run using the computer interface. Thesamples were collected as THF solutions into tared 40 mL scintillationvials.

Concentration, Azeotropic Drying, and Analysis of Recovered Materialsfrom Purifications: The THF solutions were concentrated under reducedpressure on a rotary evaporator, then the residue was azeotroped withdichloromethane (3×5 mL) to remove residual solvents. These residueswere then placed under vacuum for 12-36 hours, after which yield andpurity were determined by comparison of ¹H NMR in acetone-d₆ with astandard sample of the desired MIDA boronate and with a sample taken ofa simulated reaction mixture.

Automated Purification Detailed Protocol

-   -   A) In the background, auxiliary pump aspirates 6 mL hexanes and        delivers it to the bottom of the precipitation chamber, through        the silica gel column. This process is repeated once for a total        of 12 mL hexanes.    -   B) Primary pump aspirates 9 mL of reaction mixture from reaction        chamber bottom and returns 6 mL, through bottom, to ensure no        more than 3 mL will be delivered to the precipitation chamber.    -   C) Primary pump delivers 3 mL of reaction mixture to top of        precipitation chamber containing 12 mL hexanes. This induces        chiral, non-racemic PIDA boronate precipitation from the THF        solution. Primary pump then delivers two 10-mL plugs of dry        nitrogen to bottom of precipitation chamber (bypassing the        silica gel column) to dislodge stir bar.    -   D) Suspension in precipitation chamber is aspirated from bottom        and through silica gel column by auxiliary pump. Eluent is sent        to waste.    -   E) Steps (A)-(D) repeat three additional times to send all of        reaction mixture to precipitation chamber.    -   F) Primary pump aspirates 1.5 mL THF and delivers it to the top        of reaction chamber as a rinse. Steps (A)-(C) are repeated.    -   G) Primary pump aspirates 1.5 mL THF and delivers it to top of        reaction chamber as a rinse. Steps (B)-(C) are repeated.    -   H) Step (D) is repeated.    -   I) Steps (A)-(D) are repeated.    -   J) Step (D) is repeated.    -   K) Primary pump aspirates 6.5 mL 1.5% (v/v) MeOH in Et₂O and        delivers it to top of precipitation chamber. This process is        repeated once for a total delivery of 13 mL solvent.    -   L) Primary pump delivers two 10-mL plugs of dry nitrogen to the        bottom of the precipitation chamber (bypassing the silica gel        column) to dislodge stir bar.    -   M) Step (D) is repeated.    -   N) Steps (K)-(M) are repeated. Step (D) is repeated again.    -   O) Steps (K)-(M) are repeated twice with Et₂O instead of 1.5%        (v/v) MeOH in Et₂O. Step (D) is repeated twice more to dry out        silica gel column.    -   P) Auxiliary pump is rinsed with 2×1 mL THF to wash away any        residual MeOH. Wash THF is sent to waste.    -   Q) Auxiliary pump aspirates 6 mL THF and delivers slowly to        bottom of precipitation chamber through silica gel column. This        process is repeated once for a total of 12 mL THF.    -   R) Primary pump aspirates 5 mL dry nitrogen and delivers it to        bottom of precipitation chamber (bypassing the silica gel        column) to agitate the suspension, thus promoting mixing chiral,        non-racemic PIDA boronate dissolution. This process is done 40        times.    -   S) THF solution of chiral, non-racemic PIDA boronate is        aspirated by primary pump out of the bottom of the precipitation        chamber (bypassing the silica gel column). Solution is delivered        to the collection tube. This aspiration/delivery is repeated an        additional 5 times to ensure full transfer.    -   T) Auxiliary pump pushes residual THF in silica gel column into        bottom of precipitation chamber as a rinse.    -   U) Primary pump aspirates 5 mL dry nitrogen and delivers it to        bottom of precipitation chamber (bypassing the silica gel        column) to agitate the suspension, thus promoting mixing chiral,        non-racemic PIDA boronate dissolution. This process is done 5        times.    -   V) THF rinse is aspirated by primary pump out of bottom of the        precipitation chamber (bypassing the silica gel column).        Solution is delivered to the collection tube.

The results from this study of a wide range of structurally diverse MIDAboronates demonstrates that the hybrid precipitation/catch-and-releasepurification strategy is remarkably general.

Example 19 Aqueous Deprotection Module

The following example, while not specific to a PIDA-based system,describes procedures that, when used with a PIDA-based system, arereasonably expected to achieve similarly effective results.

Automated aqueous deprotection of phenyl MIDA boronate, trienyl MIDAboronate, and butenyl MIDA boronate was performed using the aqueousdeprotection strategy and module described above.

Automated aqueous deprotection of phenyl MIDA boronate afforded phenylboronic acid. Subsequent automated cross-coupling with the vinyl iodidebifunctional building block afforded the desired coupled product in 77%yield after manual purification. See FIG. 12A.

Automated aqueous deprotection of the trienyl MIDA boronate afforded thetrienyl boronic acid. Subsequent automated cross-coupling with the vinyliodide bifunctional building block afforded the desired coupled productin 66% yield after manual purification. See FIG. 12B.

Automated aqueous deprotection of the butenyl MIDA boronate afforded thebutenyl boronic acid. Subsequent automated cross-coupling with anisomeric mixture of the dienyl vinyl iodide bifunctional building blockafforded a 75% yield of the expected isomeric trienyl coupled productsin a 75% yield after automated purification. See FIG. 12C.

Example 20 Fully Automated Synthesis of all-Trans-Retinal Using AqueousDeprotection Module

The following example, while not specific to a PIDA-based system,describes procedures that, when used with a PIDA-based system, arereasonably expected to achieve similarly effective results.

The first deprotection tube was prepared as follows: To a new, fritted12-g cartridge (Luknova, Mansfield, Mass. 02048, Part #FC003012) wasadded trienyl MIDA boronate (345.2 mg, 1 mmol, 9 equivs). To this wasadded sodium hydroxide (120.0 mg, 3 mmol, 27 equivs). The cartridge wascapped with its female Luer-port screw cap. To this Luer port wasattached a 5-mL polypropylene syringe barrel (Henke-Sass, Wolf GmbH,Tuttlingen, Germany, 78532, Part #A5) from which the plunger had beenremoved. This first deprotection tube was wrapped with aluminum foil.

The second deprotection tube was prepared as follows: To a new, fitted12-g cartridge (Luknova, Mansfield, Mass. 02048, Part #FC003012) wasadded sodium hydroxide (40.0 mg, 1 mmol, 9 equivs). Sodium hydroxidepellets were shaved down to the correct mass with a clean razor bladeand massed quickly to minimize adsorption of atmospheric moisture. Thecartridge was capped with its female Luer-port screw cap. To this Luerport was attached a 5-mL polypropylene syringe barrel (Henke-Sass, WolfGmbH, Tuttlingen, Germany, 78532, Part #A5) from which the plunger hadbeen removed. This second deprotection tube was wrapped with aluminumfoil.

The first and second predrying tubes were prepared as follows: To a new,fitted 12-g cartridge (Luknova, Mansfield, Mass. 02048, Part #FC003012)was added Celite® 545 filter aid (800 mg, not acid-washed, AcrosOrganics, Product #349670025, Lot #A0287832). To this was addedanhydrous magnesium sulfate (2.1 g, ReagentPlus®, ≥99.5%, Sigma-Aldrich,Product #M7506, Lot #080M0246V). These two solids were mixed with aspatula until visibly homogenous. On top of the solid mixture was placeda 5-mL polypropylene syringe plunger (Henke-Sass, Wolf GmbH, Tuttlingen,Germany, 78532, Part #A5), manually cut to approximately 6.5 cm inlength. The cartridge was capped with its female Luer-port screw cap.The Luer port was covered tightly with a small square (approximately 1cm×1 cm) of aluminum foil. Each predrying tube was wrapped with aluminumfoil.

The first and second drying tubes were prepared as follows: To a new,fritted 12-g cartridge (Luknova, Mansfield, Mass. 02048, Part #FC003012)was added Celite® 545 filter aid (300 mg, not acid-washed, AcrosOrganics, Product #349670025, Lot #A0287832). To this was addedactivated molecular sieves (3.6 g, 4 Å, −325 mesh, Sigma-Aldrich,Product #688363, Lot #MKBF4010V). Molecular sieves were activated at300° C., ambient pressure, 24 h, and cooled/stored in a vacuumdesiccator under dry argon over Drierite. These two solids were notmixed. On top of the layered solids was placed a 5-mL polypropylenesyringe plunger (Henke-Sass, Wolf GmbH, Tuttlingen, Germany, 78532, Part#A5), manually cut to approximately 5.5 cm in length. The cartridge wascapped with its female Luer-port screw cap. Each drying tube was wrappedwith aluminum foil.

The first and second deoxygenating/concentrating tubes were prepared asfollows: A new, fritted 12-g cartridge (Luknova, Mansfield, Mass. 02048,Part #FC003012) was capped with its female Luer-port screw cap. Eachdeoxygenating/concentrating tube was wrapped with aluminum foil.

The first reaction tube was prepared as follows: To a new, fritted 12-gcartridge (Luknova, Mansfield, Mass. 02048, Part #FC003012) was added a4-g frit (Luknova, Mansfield, Mass. 02048, Part #FC003004). This fritwas secured, concentrically, to the 12-g cartridge frit with 26 GChromel A wire, pierced through the 12-g frit. To this reaction tube wasadded, in order, anhydrous potassium phosphate (1.39 g, 3 mmol+750 mg,27 equivs+750 mg, 97%, Alfa Aesar, Product #L15168, Lot #L02U015),palladium (II) acetate (1.9 mg, 0.0083 mmol, 2.5 mol %, ≥99.9%,Sigma-Aldrich, Product #520764, Lot #1000824996),2-dicyclohexylphosphino-2′,6′-dimethyoxy-1,1′-biphenyl (Sphos, 6.8 mg,0.017 mmol, 5 mol %, 98%, Strem Chemicals, Product #15-1143, Lot#18526300), vinyl iodide MIDA boronate (103.0 mg, 0.33 mmol, 3 equivs),and a PTFE-coated rare earth magnetic stir bar. Potassium phosphate wasfreshly ground in a 100° C. mortar and pestle. The cartridge was cappedwith its customized female Luer-port screw cap. The customized capconsists of a standard female Luer-port cap with a bent (byapproximately 45°), 1.5 inch, 18 G, disposable needle installed throughthe cap and a small ball of Kimwipe inserted into the Luer port. It isimportant remove the cored-out polypropylene plug from the inside of theneedle after installation. The cap was topped with a fritted 4-gcartridge (Luknova, Mansfield, Mass. 02048, Part #FC003004).

The precipitation tube was prepared as follows: To a new, fitted 12-gcartridge (Luknova, Mansfield, Mass. 02048, Part #FC003012) equippedwith a PTFE-coated magnetic stir bar was added Celite® 545 filter aid(150 mg, not acid-washed, Acros Organics, Product #349670025, Lot#A0287832) and 3-aminopropyl functionalized silica gel (250 mg, 40-63μm, approximately 1 mmol/g NH₂, Sigma-Aldrich, Product #364258, Lot#79096HM). The cartridge was capped with its female Luer-port screw cap.To the cartridge was added hexanes (5 mL, reagent grade) and theresulting suspension was swirled vigorously to mix the solids. The mixedsuspension was allowed to settle for approximately 5 seconds and thenthe solvent was drained by forcing a plug of ambient air through the topof the cartridge by syringe. This process firmly embeds the stir bar inthe solids to prevent stirring before the precipitation tube isutilized. This precipitation tube was wrapped with aluminum foil.

The silica gel chromatography column was prepared as follows: A silicagel chromatography column was freshly prepared from custom PTFE fittingsusing unfunctionalized silica gel. The cartridge was modeled after a 4-gcartridge (Luknova, Mansfield, Mass. 02048, Part #FC003004), but wasmade of PTFE instead of polypropylene. To a clean, fritted column wasadded silica gel. This was done by vacuum aspiration through the bottommale Luer tip fitting. This process ensured tight, even packing of thesilica gel plug. Excess silica gel was removed manually with a spatulaand a 4-g frit (Luknova, Mansfield, Mass. 02048, Part #FC003004) wasplaced on top of the silica plug. This doubly-fritted cartridge wascapped with its female Luer-port screw cap, using PTFE tape to ensure atight seal.

The second reaction vessel was prepared as follows: To a non-flame-dried7-mL glass vial equipped with a PTFE-coated magnetic stir bar was addedpalladium (II) acetate (1.2 mg, 0.0056 mmol, 5 mol %, ≥99.9%,Sigma-Aldrich, Product #520764, Lot #1000824996),2-dicyclohexylphosphino-2′,6′-dimethyoxy-1,1′-biphenyl (Sphos, 4.6 mg,0.011 mmol, 10 mol %, 98%, Strem Chemicals, Product #15-1143, Lot#18526300), and anhydrous potassium phosphate (212 mg, 1 mmol, 9 equivs,97%, Alfa Aesar, Product #L15168, Lot #L02U015). Potassium phosphate wasfreshly ground in a 100° C. mortar and pestle. This vial was sealed witha PTFE-lined septum screw cap. Through the septum was added a 1.5 inch,20 G, disposable needle connected to a dry argon gas line. Then, throughthe septum was added a 1.5 inch, 20 G, disposable needle to act as avent. The reaction vial was then flushed with dry argon forapproximately 7 min. The vent needle and then the argon needle wereremoved from the septum.

The tubes, vessels and columns described above were used as follows: SeeFIG. 13 for reaction scheme. Both deprotection tubes (wrapped withaluminum foil) were securely installed on the machine. Tubes wereinstalled by placing the tube's male Luer tip into the machine'sappropriate female Luer port and were secured with a firm downward forceand slight (less that one quarter turn) clockwise rotation. Bothpredrying tubes (wrapped and topped with aluminum foil) were securelyinstalled on the machine. Both drying tubes (wrapped in aluminum foil)were securely installed on the machine. Each drying tube was connectedto the inert gas manifold by attaching a patch line to the machine's gasmanifold and the tube's top Luer port. Patch lines are approximately12-inch lengths of tubing with male Luer-tip fittings on both ends. Bothdeoxygenating/concentrating tubes (wrapped in aluminum foil) weresecurely installed on the machine. Each deoxygenating/concentrating tubewas connected to the inert gas manifold by attaching a vented patch lineto the machine's gas manifold and the tube's top Luer port. Vented patchlines are approximately 12-inch lengths of tubing with a male Luer-tipfitting on the machine-end and a Y-connector (one port connected to theline, one port connected to a male Luer-tip fitting, and one port leftopen) on the tube-end. The first reaction tube was securely installed onthe machine (in a heating block preheated to 40° C.) and connected tothe inert gas manifold by attaching the reaction vent line to the tube'stop Luer port. The reaction tube was then covered with aluminum foil andset to stirring at 600 rpm. The silica gel column was securely installedon the machine and connected to the purification module by attaching theeluent line to the column's top Luer port. The precipitation tube(wrapped in aluminum foil) was securely installed on the machine andconnected to the purification module by placing the eluent line (fixedwith a 1.5 inch, 18 G, disposable needle) through the tube's top Luerport).

The experiment's pre-assembled code was then loaded and executed tobegin the automated sequence. The first aqueous MIDA boronatedeprotection commenced immediately. After running the first deprotection(rt, 10 min), the machine quenched and worked up the resulting boronicacid solution and then dried, deoxygenated, and concentrated it. Themachine then ran the first, slow addition, cross-coupling reaction (40°C., 8 h total) and purified the resulting coupled product. The machinethen ran the second aqueous MIDA boronate deprotection (rt, 10 min) andsubsequently quenched, worked up, dried, deoxygenated, and concentratedthe resulting boronic acid solution.

Approximately 5 minutes before the second cross-coupling began, thesecond reaction vessel was placed in an aluminum block (at roomtemperature) on a stir plate. An inert gas vent line (fixed with a 1.5inch, 20 G, disposable needle) was connected, through the septum. Thereaction tube was then covered with aluminum foil and set to stirring at600 rpm. Separately, into a non-flame-dried 1.5-mL glass vial was addedthe aldehyde (16.6 mg, 0.11 mmol, 1 equiv). The vial was sealed with aseptum screw cap and to this was added 100 μL deoxygenated dry THF froma 100 μL, gas tight, fixed needle, glass syringe. The vial was manuallygently agitated to dissolve the aldehyde and then was added to thereaction vial with the same syringe. The remaining residual aldehyde wasquantitatively transferred to the reaction vial with 2×50 μL ofdeoxygenated dry THF using the same syringe. As the machineautomatically deoxygenated the reaction addition line (fixed with a 1.5inch, 22 G, disposable needle), it was connected to the reaction vessel,through the septum. The machine then ran the second, fast addition,cross-coupling reaction (rt, 3 h).

At the end of 3 hours, the reaction vial was removed from the machineand the crude reaction mixture was filtered through a 1-cm pad ofCelite® packed in a pipette. The reaction vial was washed with 3×2 mLdry THF and these washings were filtered through the Celite® pad. Thepad was then washed with 3×2 mL dry THF. The resulting clear dark yellowfiltrate was concentrated in vacuo (rt, 80 Torr), azeotroped with 3×5 mLdichloromethane (rt, 80 Torr), and residual solvent was removed on highvacuum (30 min, 200 mTorr) to afford a dark yellow/orange sticky solid.This crude product was manually purified by silica gel flashchromatography to afford a mixture of all-trans-retinal: 13-cis-retinalin a ratio of 1:0.55 in a combined total 30% yield.

Example 21 Automated Purification of a Simulated Reaction MixtureContaining a PIDA Boronate

Pre-activation of the Catalyst Solution: Palladium(II) acetate (4.4 mg,0.01959 mmol, 5 mol %) and SPhos (7.7 mg, 0.01875 mmol, 5 mol %) werecombined in an 8 mL scintillation vial equipped with a PTFE-coatedmagnetic stir bar and placed under a nitrogen atmosphere. THF (5 mL) wasadded to generate a catalyst stock solution (with respect topalladium(II) acetate), and it was stirred vigorously for 30 min at roomtemperature to generate an orange, yellow, or clear solution. After thisactivation process, 1 mL of the catalyst stock solution was added to thesolution in the polypropylene cartridge containing the simulatedreaction mixture.

Preparation and Installation of Simulated Reaction Chamber: A new fitted12 g Luknova polypropylene cartridge was charged with styrenyl PIDAboronate (28.6 mg, 0.075 mmol, 1 eq), 4-methylbenzene boronic acid (10.2mg, 0.075 mmol, 1 eq), and THF (10 mL). After addition of thepre-activated catalyst solution, the cartridge was installed into theLuer fittings in the reaction block of the automated synthesizer. Onceall cartridges were in place, the automated purification routine was runusing the computer interface. The samples were collected as THFsolutions into tared 40 mL scintillation vials.

Concentration, Azeotropic Drying, and Analysis of Recovered Materialfrom Purification: The THF solution was concentrated under reducedpressure on a rotary evaporator, then the residue was azeotroped withdichloromethane (3×5 mL) to remove residual solvents. The residue wasthen dried in vacuo. The percentage recovery was determined toapproximately 35%. SPhos and the boronic acid were purified away fromthe PIDA boronate; however an unknown side product was formed during thepurification procedure as indicated in the NMR of the purified product(FIG. 14). The ¹H NMR of the purified product in acetone-d6 was comparedwith a sample of the stimulated reaction mixture before purification.

Example 22 Automated Hydrolysis of a PIDA Boronate with Aq. NaOHProcedure

A Luknova cartridge (12 g) was charged with styrenyl PIDA boronate (0.2mmol, 1 equiv) and solid sodium hydroxide (0.6 mmol, 3 equiv). Automatedaqueous deprotection, drying and concentration of the resulting boronicacid solution was then started using the computer interface. The boronicacid solution was then further concentrated under reduced pressure witha rotary evaporator. ¹H NMR analysis of the residue showed a mixture ofstyrenyl boronic acid, the corresponding boroxine, and some PIDA ligand.No PIDA boronate starting material was found in the analysis.

INCORPORATION BY REFERENCE

All publications and patents mentioned herein are hereby incorporated byreference in their entirety as if each individual publication or patentwas specifically and individually indicated to be incorporated byreference. In case of conflict, the present application, including anydefinitions herein, will control.

EQUIVALENTS

While specific embodiments of the subject invention have been discussed,the above specification is illustrative and not restrictive. Manyvariations of the invention will become apparent to those skilled in theart upon review of the specification. The appended claims are notintended to claim all such embodiments and variations.

1-144. (canceled)
 145. A method of deprotecting a pinene-derivediminodiacetic acid (PIDA) boronate, comprising: contacting a solutioncomprising the chiral, non-racemic PIDA boronate and a solvent with asolid-supported ammonium hydroxide reagent, thereby deprotecting thechiral, non-racemic PIDA boronate and forming a boronic acid and a PIDA.146. The method of claim 145, wherein the solvent comprises THF. 147.The method of claim 145, wherein the solid-supported ammonium hydroxidereagent binds the PIDA.
 148. The method of claim 145, further comprisingthe steps of removing the solvent by filtration, leaving the boronicacid and PIDA ligand trapped inside the solid-supported ammoniumhydroxide reagent; and adding additional solvent.
 149. The method ofclaim 148, wherein the additional solvent is THF.
 150. The method ofclaim 145, further comprising washing the solid-supported ammoniumhydroxide reagent with an organic solution comprising an organic solventand an acid in a quantity greater than that needed to neutralize thesolid-supported ammonium hydroxide reagent, thereby eluting the boronicacid.
 151. The method of claim 150, wherein the organic solvent is THF.152. The method of claim 151, wherein the acid is acetic acid.
 153. Themethod of claim 152, further comprising treating the eluted boronic acidwith base to neutralize the acetic acid.
 154. The method of claim 153,wherein the base is potassium carbonate.
 155. The method of claim 145,further comprising washing the solid-supported ammonium hydroxidereagent with a 1,4-dioxane solution comprising hydrochloric acid,thereby eluting the boronic acid.
 156. The method of claim 145, whereinthe solid-supported ammonium hydroxide reagent is a strong base anionexchange resin.
 157. The method of claim 145, wherein thesolid-supported ammonium hydroxide reagent is a strong base, type 1,anionic, macroreticular polymeric resin based on crosslinked styrenedivinylbenzene copolymer containing quaternary ammonium groups. 158-164.(canceled)